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Impact of diverse cropping patterns on greenhouse gas emissions: Assessing energy Use efficiency in Rangpur District, Bangladesh
No full textBangladesh relies heavily on rice-based cropping systems to maintain food security. Additionally, crop diversification, which also contribute to enhance agricultural productivity and profitability in a nation with a high population density and scarce arable land. However, greenhouse gas emissions from the agricultural sector is remain unclear. On-farm research trials briefly summarize the results of greenhouse gas emissions from a diversified cropping systems after one full cropping cycle. This trial was conducted in the Chargonai and Shibdeb villages of the Rangpur district, addressing total global warming potential, total energy use, and emissions intensity, which are crucial for achieving TAFSSA’s goals. Therefore, the trial aims to emphasize climate change effects to identify strategies to mitigate greenhouse gas emissions from agricultural land.18 page
Development of a qPCR assay for species-specific detection of the tar spot pathogen Phyllachora maydis
No full textPhyllachora maydis is a fungal plant pathogen that causes tar spot of corn (Zea mays) in North and South America, causing devastating yield losses under favorable conditions. Although the causal agent is relatively easy to diagnose via macroscopic and microscopic observations, other diseases and conditions, such as insect frass, have been mistaken for tar spot of corn. Furthermore, conidia and ascospores in isolation can be difficult to visually distinguish from other fungi, and the development of signs and symptoms of the disease may not be observed until 12 to 20 days after infection. Therefore, we developed a TaqMan quantitative polymerase chain reaction (qPCR) assay for the detection and quantification of this pathogen to be used for diagnostics and airborne spore quantification. The assay was designed for the internal transcribed spacer region of P. maydis. The specificity of the assay was confirmed and tested against various nontarget Phyllachora species, corn pathogens, endophytes, and P. maydis samples from several states in the Midwest and from Mexico. The detection limit of this assay was determined to be 100 fg of genomic P. maydis DNA. To demonstrate the transferability of this technology, the assay was tested in different labs using various qPCR thermal cyclers. This assay can be used in downstream research involving latency period, disease prediction, and diagnostics.61-7
Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.)
No full textThe suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and GxE variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels
Chapter 11. Genomic insights on global journeys of adaptive wheat genes that brought us to modern wheat
No full textSince its first cultivation, hexaploid wheat has evolved, allowing for its widespread cultivation and contributing to global food security. The identification of adaptive genes, such as vernalization and photoperiod response genes, has played a crucial role in optimizing wheat production, being instrumental in fine-tuning flowering and reproductive cycles in response to changing climates and evolving agricultural practices. While these adaptive genes have expanded the range of variation suitable for adaptation, further research is needed to understand their mechanisms, dissect the pathways involved, and expedite their implementation in breeding programs. By analyzing data across different environments and over time, Meta-QTL analysis can help identify novel genomic regions and facilitate the discovery of new candidate genes. This chapter reports on two previously unknown Meta-QTL regions, highlighting the potential for further exploration in this field. Moving forward, it will be increasingly important to expand our understanding of how genetic regions influence not only flowering time but also other developmental traits and their responses to environmental factors. Advances in gene-based modeling hold promise for describing growth and development processes using QTL and other genomic loci analysis. Integrating these findings into process-based crop models can provide valuable insights for future research. Overall, the study of adaptive genes and their impact on wheat production represents a vital area of research that continues to contribute to global food security.213-23
Transmission pathways for the stem rust pathogen into Central and East Asia and the role of the alternate host, barberry
No full textAfter many decades of effective control of stem rust caused by the Puccinia graminis f.sp. tritici, (hereafter Pgt) the reported emergence of race TTKSK/Ug99 of Pgt in Uganda reignited concerns about epidemics worldwide because similar to 90% of world wheat cultivars had no resistance to the new race. Since it was initially detected in Uganda in 1998, Ug99 variants have now been identified in thirteen countries in Africa and the Middle East. Stem rust has been a major problem in the past, and concern is increasing about the risk of return to Central and East Asia. Whilst control programs in North America and Europe relied on the use of resistant cultivars in combination with eradication of barberry (Berberis spp.), the alternate host required for the stem rust pathogen to complete its full lifecycle, the focus in East Asia was principally on the use of resistant wheat cultivars. Here, we investigate potential airborne transmission pathways for stem rust outbreaks in the Middle East to reach East Asia using an integrated modelling framework combining estimates of fungal spore deposition from an atmospheric dispersion model, environmental suitability for spore germination, and crop calendar information. We consider the role of mountain ranges in restricting transmission pathways, and we incorporate a representation of a generic barberry species into the lifecycle. We find viable transmission pathways to East Asia from the Middle East to the north via Central Asia and to the south via South Asia and that an initial infection in the Middle East could persist in East Asia for up to three years due to the presence of the alternate host. Our results indicate the need for further assessment of barberry species distributions in East Asia and appropriate methods for targeted surveillance and mitigation strategies should stem rust incidence increase in the Middle East region
Climate smart machinery - enhancing smallholder agriculture in a changing climate
No full text23 slide
Genome-wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes
No full textSpot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using field screening and genome-wide association mapping strategies. Field experiments were conducted in Agua Fria, Mexico, during the 2019–2020 and 2020–2021 cropping seasons. A wide range of phenotypic variation was observed among genotypes tested during both years. Twenty SNP markers showed significant association with spot blotch resistance on 15 chromosomes, namely, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7B. Of these, two consistently significant SNPs on 5A, TA003225-0566 and TA003225-1427, may represent a new resistance quantitative trait loci. Further, in the proximity of Tsn1 on 5B, AX-94435238 was the most stable and consistent in both years. The identified genomic regions could be deployed to develop spot blotch-resistant genotypes, particularly in the spot blotch-vulnerable wheat growing areas
Evolution of Puccinia triticina Eriksson, the cause of leaf rust of durum wheat in Mexico
No full textDuring the 2016-17/Autumn-Winter cycle in Southern Sonora, Mexico there was an epidemic of leaf rust, caused by the fungus Puccinia triticina Eriksson in the wheat variety Cirno C2008, resistant until the previous immediate cycle. Visible lesions appeared in early February 2017, gradually increasing the number of infected fields. Leaves with signs of the disease were collected in commercial fields and trap nurseries for analysis in the greenhouse. After purifying and obtaining monopustular isolates, the spores were increased, and differential plants for leaf rust were inoculated. In this way, the presence of a new race initially called BBG/BPCam, product of the evolution of BBG/BP identified during 2008, was determined affecting the varieties Banamichi C2004 and Jupare C2001. Two additional sets of differential plants were used to differentiate the two races,. The monopustular isolates of all samples indicated the presence of a new race called BBG/BPCJ, with the new nomenclature, and that evolved through a simple mutation in the race BBG/BP (BBG/BPCG with the new nomenclature) with virulence on the LrCam gene present in the variety Cirno C2008 and its progenitor Camayo. The analysis of the differentials and other controls at the seedling stage, indicated the absence of other changes in the pathogen virulence, apart from the aforementioned. Lines carrying Lr3 and Lr61, although susceptible to other races, remained effective against BBG/BPCJ. The genotypes where the presence of Lr14a was postulated and the lines of the cross Altar 2*/TcLr14a remained resistant to BBG/BPCJ in both seedling and adult plant. Since the introduction of BBB/BNGQ (BBG/BN) in Mexico in 2001, this rust race has continued to evolve and overcome specific resistance genes in durum wheat.Durante el ciclo otoño-invierno/2016-17 en el sur de Sonora, México, se presentó una epidemia de roya de la hoja, causada por el hongo Puccinia triticina Eriksson en la variedad de trigo Cirno C2008, resistente hasta el ciclo inmediato anterior. Las lesiones visibles aparecieron a inicios de febrero de 2017, aumentando gradualmente el número de campos infestados. Se colectaron hojas con signos de la enfermedad en campos infectados y viveros trampa para análisis en invernadero. Después de purificar y hacer aislamientos monopustulares, se incrementaron las esporas y se procedió a inocular plantas diferenciales para roya de la hoja. De esta forma, se determinó la presencia de una nueva raza denominada inicialmente BBG/BPCam, producto de la evolución de BBG/BP identificada durante 2008, y que afectó a las variedades Banámichi C2004 y Júpare C2001. Para diferenciar ambas razas se utilizaron dos juegos adicionales de plantas diferenciales. Los aislamientos monopustulares de todas las muestras indicaron la presencia de una nueva raza denominada BBG/BPCJ, con la nomenclatura nueva, y que evolucionó a través de una mutación simple en la raza BBG/BP (BBG/BPCG con la nueva nomenclatura) con virulencia en el gen LrCam presente en la variedad Cirno C2008 y en su progenitor Camayo. El análisis de las diferenciales y otros testigos, en estado de plántula, indicaron ausencia de otros cambios en la virulencia del patógeno, aparte del ya mencionado. Las líneas que llevan Lr3 y Lr61, aunque susceptibles a otras razas, siguieron siendo efectivas contra BBG/BPCJ. Los genotipos donde se postuló la presencia de Lr14a y las líneas de la cruza Altar 2*/TcLr14a permanecieron resistentes a BBG/BPCJ, tanto en plántula como en planta adulta. Desde la introducción de BBB/BNGQ (BBG/BN) en México en 2001, esta raza ha seguido evolucionando y venciendo genes de resistencia específicos en trigo cristalino.3-1
