International Crops Research Institute for the Semi-Arid Tropics
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Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding
Get PDFPearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K middensity SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet
Shaping food environments to support sustainable healthy diets in low and middle-income countries
Get PDFThe global ambitions to end hunger, achieve food security and improved nutrition, and promote sustainable agriculture demand a complex transition of the current food environments for enabling sustainable healthy diets. The food environments in Low and Middle-Income Countries (LMICs) have been experiencing rapid and dynamic transitions across the globe, necessitating a system-level thinking and systemic approach to understand opportunities for improvement. There is a need for valid, reliable measures of food and nutrition environments for reorienting thinking and data collection toward determinants of food demand, especially the food environment components, which are critical to understand the transforming food systems. Food environment transformations are urgently required to provide consumers with more
Crop Microbiome for Sustainable Agriculture in Special Reference to Nanobiology
No full textThe microbial population surrounding plant is regarded as the crop microbiome and they are essential in crop development and sustenance. Specifically, the plant growth-promoting microbes play a key role as growth enhancers and disease suppressors. These plants associated microbiomes are often considered as one of the essential agricultural components toward an enhanced crop yield. This has led to a wide range of nanotechnological applications on the agricultural systems to boost crop output. In this scenario, the nanoparticles are largely seen interacting with the crop microbiomes and the plant systems. Hence, in the present chapter, the role and response of these crop microbiomes and nanoparticles will be discussed in detail. From the point of application of these nanoparticles, their effect on the plant growth-promoting bacterial systems and to their biosynthesis utilizing the crop microbiomes will be explored. Nanomaterials interaction with root colonizing microbes often promised enhanced plant health during both abiotic and biotic stress conditions through rhizobacterial metabolite changes. Nanotechnology, being a new frontier in the modern agriculture practices, the challenges of nanoparticle dosage, cost efficiency, and their footprint in the agricultural soils over a long time was one of the vital areas to observe. On the other hand, nanoparticles are widely reported to enhance the plant growth-promoting and defense traits of the crop microbiomes and play a key role in global food production. The present chapter discusses the key features of crop microbiomes, their response to nanoparticles, and together how they could influence the crop yield and biotic stress resistance
The Progression in Developing Genomic Resources for Crop Improvement
Get PDFSequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis technique
Impacts of fertilization management strategies on improved sorghums varieties in smallholder farming systems in Mali: Productivity and profitability differences
Get PDFSorghum is an important cereal crop cultivated by smallholder farmers of Mali, contributing significantly to their food demand and security. The study evaluated different fertilization strategies that combined organic and inorganic fertilizer applications with three sorghum varieties. The experiments were conducted over three cropping seasons (2017–2019) in three sites (Bamako, Bougouni, and Koutiala respectively) within the Sudanian region of Mali. Our results showed a significant effect of season, variety, and fertilization strategies on grain and stalk yields. Grain yield increased by 8–40% in Koutiala, 11–53% in Bougouni, and 44–110% in Bamako while the average stalk yield was above 5000 kg h
Groundnut Value Chain Study in India with Special Emphasis on High Oleic Cultivars
Get PDFThe market structure in developing countries has been rapidly changing since 1950, particularly in the agriculture and food sector Crop improvement scientists have immensely contributed to the Green Revolution by fulfilling actors’ demands in the cereal food supply chain. Higher growth in production enabled the country not only to achieve self-sufficiency but also to create primary and secondary markets. This increased productivity has moved agriculture from subsistence to market-led systems where markets were influenced by emerging segments and their needs and preferences. A growing population, consumerism, urbanization, changing lifestyles, etc., have created an opportunity for stakeholders in the market chain to express their needs and preferences precisely. Reciprocally, this deviation of work – from developing agro-climatic plant to creating market-led varieties – has formed an avenue for crop improvement scientists to collect needs and preferences from all their value chain actors (growers to consumers), and eventually translate them into breeding decisions (Ragot et al. 2018), i.e., developing a demand-led plant variety design (Yao et al. 2017)
The demand-led breeding approach enabled crop improvement scientists to develop higher-performing varieties that meet customer requirements and market demand (Persley et al. 2017)4. However, markets in developing countries were characterized by dual value chains (informal and formal/modern) where information flow is in both directions, i.e., where markets inform producers of price, quantity and quality needs, product handling, and technology options, while producers inform processors and markets on production quantities, locations, timing and production issues (Norton 2014)5. Hence a better understanding of the structure of crop value chains is required for designing a new variety; and goals and objectives have to be set based on the needs of the value chain actors or with a specific focus on individual trait improvement (Pangirayi et al. 2017)6. To be more precise, scientists should have an understanding on the various categories of clients in the value chain, their preferences, and preparedness to pay for it (Pangirayi et al. 2017). This research note presents the preferences of products and the preparedness to pay by the value chain actors of groundnut in India with special focus on Gujarat State. The end objective of the research is to help the breeders in a basic understanding of groundnut market traits and the scope for new varietal designing or further improvements in existing varieties. Furthermore, feedback about high oleic cultivars were also captured through brainstorming and summarized in this report
Contributions of fine mineral particles and active Al/Fe to stabilization of plant material in neutral-to-alkaline soils of Indo-Gangetic Plain
Get PDFFactors controlling organic carbon stabilization are elusive in neutral-to-alkaline soils, thereby hindering the
assessment of carbon sequestration potential across vast agricultural regions like the Indo-Gangetic Plain (IGP).
This study investigated controls over mineralization and stabilization of added organic matter in tropical neutralto-
alkaline soils with low organic carbon (SOC). Using topsoil and subsoil samples from 12 sites of upper-tolower
IGP, we conducted a one-year incubation with and without adding 13C-labeled maize material. We
tracked CO2 release and residual C remaining in soil organic matter fractions (free, occluded particulate (oPOM),
and mineral-associated organic matter (MAOM)) and analyzed organic matter molecular compositions in incubated
soils using pyrolysis-GC/MS. Our results revealed that 48 ± 7 % of added maize C was mineralized, mostly
within the first 70 days. Higher active Al/Fe, notably Al, retarded primary maize mineralization by facilitating
aggregation. High SOC content and SOC saturation degree resulted in more maize mineralization. The disappearance
of maize-unique compounds (e.g., neophytadiene) revealed substantial degradation of added maize.
Regarding SOC composition, maize addition increased the relative abundance of fatty acids and decreased that of
N-containing compounds. Most residual maize-derived C was found in stabilized fractions, MAOM (77 ± 15 % of
residual maize C) and oPOM (8 ± 4 %). Clay fraction contributed to most maize-derived C stabilization as MAOM
(path coefficient (β) = 0.81**). Moreover, the significant correlation (P < 0.001) between maize-derived oPOM C
and active Al/Fe or clay + silt suggested that active Al/Fe contributed to the stabilization of maize-derived C as
oPOM (β = 0.62***) probably by bonding clay and silt particles to form stable aggregates since active Al/Fe
content was low (<14 cmol kg-1). Our study highlighted the importance of active Al/Fe in stabilizing SOC, by
promoting aggregation and retarding degradation of residue-derived C in neutral-to-alkaline soils
AMMI and GGE Biplot Analyses for Mega-Environment Identification and Selection of Some High-Yielding Oat (Avena sativa L.) Genotypes for Multiple Environments
Get PDFThis paper reports an evaluation of eleven oat genotypes in four environments for two consecutive years to identify high-biomass-yielding, stable, and broadly adapted genotypes in selected parts of Ethiopia. Genotypes were planted and evaluated with a randomized complete block design, which was repeated three times. The additive main effect and multiplicative interaction analysis of variances revealed that the environment, genotype, and genotype–environment interaction had a significant (p ≤ 0.001) influence on the biomass yield in the dry matter base (t ha−1). The interaction of the first and second principal component analysis accounted for 73.43% and 14.97% of the genotype according to the environment interaction sum of squares, respectively. G6 and G5 were the most stable and widely adapted genotypes and were selected as superior genotypes. The genotype-by-environment interaction showed a 49.46% contribution to the total treatment of sum-of-squares variation, while genotype and environment effects explained 34.94% and 15.60%, respectively. The highest mean yield was obtained from G6 (12.52 kg/ha), and the lowest mean yield was obtained from G7 (8.65 kg/ha). According to the additive main effect and multiplicative interaction biplot, G6 and G5 were high-yielding genotypes, whereas G7 was a low-yielding genotype. Furthermore, according to the genotype and genotype–environment interaction biplot, G6 was the winning genotype in all environments. However, G7 was a low-yielding genotype in all environments. Finally, G6 was an ideal genotype with a higher mean yield and relatively good stability. However, G7 was a poor-yielding and unstable genotype. The genotype, environment, and genotype x environment interaction had extremely important effects on the biomass yield of oats. The findings of the graphic stability methods (additive main effect and multiplicative interaction and the genotype and genotype–environment interaction) for identifying high-yielding and stable oat genotypes were very similar
Scaling-up water management interventions for rainfed agriculture in the Ethiopian Highlands: status, issues, and opportunities
Get PDFEthiopia is the second most populous country in Africa with more than 110 million people. The capacity to feed its rapidly growing population largely depends on rainfed agricultural production systems, in a range of agro climatic regions from arid and semiarid lowlands to temperate
highlands. Agriculture is undermined by both severe land degradation and high inter- and intra-seasonal rainfall variability. As a result, the current average productivity of rainfed farming remains low (1.7 t ha-1 for pulses and 2.7 t ha-1 for cereals). This is despite a slow yield increase (e.g. about 1.5 t ha-1 for cereals and 1 t ha-1 for pulses) due to the introduction of new crop cultivars,
fertilizers and management practices. Recognising the large yield gap in rainfed systems, the Ethiopian government has, since 1970, initiated a number of public welfare programs. These have involved various natural resource management
programs with a special focus on agricultural water management (AWM) in Sustainable Land Management Projects (SLMP). SLMPs, centered around rainfed production systems, have been implemented to address land degradation, enhance crop and livestock productivity, and improve household incomes. Integrated resource management approaches have helped local communities obtain tangible benefits from AWM,
and strengthened a number of ecosystem services, when compared to a sectoral approach. In the last 15 years, through SLMP 1 and 2, more than 2% of agricultural fields, and communal rainfed land, in Ethiopia, has been subject to AWM and sustainable land management. This has benefitted
around 1.4 million households and supported environmental sustainability. Over 430,000 people have also benefited from related income generating activities. However, systematic data on various aspects of AWM is required to obtain a clear understanding of the overall impact of these interventions. This study proposes following a landscape approach, in order to realize the full potential of diverse AWM interventions, and a consortium approach to capacity building to achieve large scale, system level outcomes