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RGB imaging and computer vision-based approaches for identifying spike number loci for wheat
No full textThe spike number (SN) is an important trait that significantly impacts grain yield in wheat. Manual counting of SN is time-consuming, hindering large-scale breeding efforts. Hence, there is an urgent need to develop efficient and accurate methodologies for SN counting. A YOLOX algorithm was used to determine the optimal growth stage for developing wheat spike detection models among recombinant inbred lines (RILs) across Zhongmai 175 x Lunxuan 987 and a diverse panel of 166 cultivars. We subsequently increased the precision of spike identification by developing a new YOLOX-P algorithm that incorporates the convolutional block attention module and increasing the resolution of the input images. We also used these SN data to identify underlying loci in the Zhongmai 578 x Jimai 22 RIL population. The results revealed that the late grain-filling stage presented the highest precision among the SN detection models, with accuracies ranging from 91.8 to 95.02 %. The improved YOLOX-P algorithm demonstrated higher mean average precision scores (5.30-5.99 %) and F1 scores (0.06) than did the YOLOX algorithm when it was applied to the same subsets. Three new SN loci, namely, QSN.caas-4A2, QSN.caas-4D and QSN.caas-5B2, were identified using the 50k SNP arrays. Two kompetitive allele-specific PCR markers linked with QSN.caas-4A2 and QSN.caas-5B2 were developed, and their genetic effects were validated in a diverse panel of 166 cultivars. These findings provide useful tools for high-throughput identification of SNs and novel loci in wheat
Learning from positive deviants' practices to improve the performance of mixed crop-livestock systems in Zimbabwe
No full textCONTEXT: In Zimbabwe, farm productivity of smallholder farmers practising mixed crop-livestock farming is hindered by climate variability, inadequate nutritious feeds, poor soil fertility, and resource trade-offs. Despite these challenges, positive deviants (PDs) within these communities achieve better outcomes using resources similar to those of other farmers. OBJECTIVE: This study sought to identify crop-livestock practices that enable PDs to outperform low-efficiency farms (LEFs) and to compare their farm productivity (energy output), nutrient quantities added to croplands, gross margins and return on investment (ROI) from crop production. METHODS: Data from a survey conducted in Mutoko and Buhera districts of Zimbabwe in 2021 were used to derive a farm typology per district and identify PDs and LEFs within farm types. Selected farms were subjected to detailed surveys to identify their specific practices. RESULTS AND CONCLUSIONS: Compared to LEFs, PD farmers achieved significantly greater crop productivity — by 86 %, 89 % and 28 % — and livestock productivity — by 156 %, 101 % and 136 % on better-off, average and poorly-resourced farms, respectively. PDs had larger cropping areas (on average 42 % more) and owned more livestock (39 % more TLUs) than LEFs, but this does not fully explain differences in productivity. PDs used more inputs (fertilizer, labour and others) for crop production than LEFs and added more carbon and nitrogen to their soils. In both districts, PDs consistently outperformed LEFs in gross margins and ROI. The differences in economic performance between PDs and LEFs were more pronounced among the better-off farmers. Key practices contributing to PDs' success included recommended fertilizer use, timely operations, livestock supplementary feeding, fodder production, and adherence to extension advice. Financial shortages for the purchase of seeds, fertilizers, and veterinary drugs and poor access to information are potential hindrances to the adoption of PD practices by LEF farmers. SIGNIFICANCE: The combination of a farm typology and the PD approach helped to tailor recommendations to farms differing in resource-endowment, based on successful practices implemented in the region
Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices
No full textChanges in soil characteristics due to varying farming practices can modify the structure of bacterial communities. However, it remains uncertain whether bacterial groups that break down organic material are similarly impacted. We examined changes in the bacterial community by pyrosequencing the 16S rRNA gene when young maize plants, their neutral detergent fibre fraction, or urea were applied to an Australian Vertisol. This soil was managed with either conventional tillage with continuous cotton, minimum tillage with continuous cotton, or a wheat-cotton rotation. The soil organic carbon content was 1.4 times higher in the wheat-cotton rotation than in the conventional tillage with continuous cotton treatment. Approximately 41.6% of the organic carbon was added with maize plants, and 13.1% of the neutral detergent fibre fraction was mineralized after 28 days. The application of young maize plants and the neutral detergent fibre fraction significantly altered the bacterial community and the presumed metabolic functional structure, but urea did not. Many bacterial groups, such as Streptomyces, Nocardioides, and Kribbella, and presumed metabolic functions were enriched by the application of organic material, but less so by urea. We found that a limited number of bacterial groups and presumed metabolic functions were affected in an irrigated Vertisol by the different cotton farming systems, but many were strongly affected by the application of maize plants or its neutral detergent fibre
Spatiotemporal variation of crop diversification across Eastern Indo Gangetic plains of South Asia
No full textSouth Asia's Eastern Indo-Gangetic Plain (EIGP) of India, Nepal, and Bangladesh is home to approximately 450 million people and predominantly rely on agriculture for livelihood. Agriculture is highly cereal-centric in EIGP. Increasing crop diversification within the EIGP region could improve agricultural sustainability, but knowledge of the spatiotemporal patterns of crop diversification and how it varies across EIGP countries is limited. In this study, we used historical sub-national crop data from India (1966–2022), Nepal (2000–2022), and Bangladesh (1971–2022) to measure crop diversification and compare it with the existing sub-district level scale. Crop diversification was measured using the Herfindahl-Hirschman Index (HHI). We found a noticeable increase in overall crop diversification in EIGP during this period but with spatiotemporal variations between the countries and seasons. Furthermore, while comparing sub-national patterns with existing sub-district patterns, we found opposing trends. Our data suggest that sub-national diversification patterns are an aggregate measure that may obscure the diversification pattern at the district, sub-strict, and even community level diversification. Measurements of sub-national crop diversification may appear to have moderate diversification overall, but this could result from some districts having high levels of diversification while others more oriented towards monocropping and a lack of diverse crop rotations. Our findings provide a new approach and a baseline of crop diversification in the EIGP for future research and interventions agricultural policy and development planners
Molecular screening of septoria-resistant genes in historical Turkish bread wheat germplasm using the validated gene specific SSR markers
No full textSeptoria tritici blotch (STB), caused by Zymoseptoria tritici, poses a significant threat to global wheat production, particularly in T & uuml;rkiye. Resistance breeding is the most sustainable and effective disease control method. Molecular markers, especially simple sequence repeat (SSR) markers are extensively employed in wheat breeding to enhance the efficacy. The primary objective of this study was to identify Stb resistance genes among 143 historical registered Turkish bread wheat genotypes released as commercial cultivars between 1963 to 2014, using 16 closely linked SSR markers. The findings revealed substantial genetic variation among the screened cultivars, with the Stb3 gene being the most prevalent, identified in 89.51% of the samples. Other notable resistant genes included Stb13 (71.32%), Stb4 (43.33%), and Stb11 (41.25%). Cultivars Porsuk-2811, Porsuk-2853, and Porsuk-2868 exhibited the highest level of resistance to STB, with 10 resistance genes detected. Of the 143 cultivars screened, 10 were found to carry a total of nine Stb genes, while two cultivars were observed to possess only a single resistance gene. The study identified 23 wheat cultivars harboring 8-10 Stb resistance genes, which are highly recommended for future wheat breeding programs and gene pyramiding strategies to combat Z. tritici. This research provides critical insights for national breeding programs, supporting the development of resilient and high-yielding wheat varieties resistant to STB.89-10
Enhancing food security in an era of rising fertilizer prices: Evaluation of an intervention promoting mungbean adoption in Nepal
No full textThe improved food security in Asia that has facilitated the region's development progress depends on nitrogenous fertilizers. Rising prices and shortages of imported fertilizer have prompted countries to explore alternative sources of crop nitrogen, including diversification with legumes. We evaluate an intervention in Nepal that promoted mungbean adoption. Our doubly robust impact evaluation approach accounts for nonrandom patterns of adoption related to livestock rearing, participation in agricultural cooperatives and training, and greater irrigated land use. Adopters growing mungbean for the 2-year study period showed an average increase of 20 kilograms (kg) in their annual consumption of mungbean-based foods, applied almost 40kg per hectare (ha) less fertilizers to their rice crops, and obtained an additional 280kg in rice yield per ha. Hence, agricultural innovations that use legumes such as mungbean can help promote sustainable intensification of cereal-based production systems, while enhancing food security and reducing balance-of-payments issues for the countries dependent on fertilizer imports.179–20
Identification of resistance sources and genomic regions regulating Septoria tritici blotch resistance in South Asian bread wheat germplasm
No full textThe Septoria tritici blotch (STB) [Zymoseptoria tritici (Desm.)] of wheat (Triticum aestivum L.) is characterized by its polycyclic and hemibiotrophic nature. It is one of the most dangerous diseases affecting wheat production worldwide. Durable resistance is largely decided by the combined effect of several quantitative trait loci (QTLs) having a minor effect. Currently, STB is not important in South Asia. However, STB expanding and wider adaptability, changing climatic conditions, and agronomic practices can create a situation of concern. Therefore, dissection of the genetic architecture of adult-plant resistance with genome-wide association mapping and selection of resistant sources for adult plant STB resistance were carried out on a panel of South Asian germplasm. We discovered the 91 quantitative trait nucleotides (QTNs) associated with STB resistance; 23 QTNs were repetitive across the different years and models. Many of these QTNs could differentiate the mapping panel into resistant versus susceptible groups and were linked to candidate genes related to disease resistance functions within linkage disequilibrium blocks. The repetitive QTNs, namely, Q.CIM.stb.2DL.2, Q.CIM.stb_dh.2DL.3, Q.CIM.stb.2AL.5, and Q.CIM.stb.7BL.1, may be novel due to the absence of co-localization of previously reported QTLs, meta-quantitative trait loci, and STB genes. There was a perfect negative correlation between the stacking of favorable alleles and STB susceptibility, and STB resistance response was improved by ∼50% with the stacking of ≥60% favorable alleles. The genotypes, namely, CIM20, CIM56, CIM57, CIM18, CIM44, WK2395, and K1317, could be used as resistant sources in wheat breeding programs. Therefore, this study could aid in designing the breeding programs for STB resistance before the onset of the alarming situation of STB in South Asia
Accelerating genetic gain through early-stage on-farm sparse testing
No full textMost African crop breeding programs conduct early-stage selection at very few research stations, which may not reflect smallholder farm conditions. Early-stage on-farm sparse testing utilizes genomic relationships to shift selection from research stations to hundreds of farms in the target population of environments, facilitating increased genetic gain in farmers’ fields.17-2
Tester selection for combining ability estimation of storage root yield and sweetpotato virus disease in sweetpotato breeding
No full textGeneral combining ability (GCA) is the major selection criterion for new sweetpotato (Ipomoea batatas) parents in a reciprocal recurrent selection (RRS) scheme. Here we aimed to estimate GCA and specific combining ability (SCA) by using 16 potential testers involved in an 8 x 8 partial diallel and propose a procedure to identify testers in sweetpotato breeding. Data on storage root yield in tons per hectare (rytha), and sweetpotato virus disease (vir2) from 64 families (1,913 clones) were collected in five trials at two locations in Uganda. The estimates of the female GCA accounted for the largest additive genetic variation for storage root yield compared to the male GCA for both traits. Mid-parent heterosis ranged from - 6.2 to 7% for rytha, and - 1.1 to 1.3% for vir2 in the progeny families. A stepwise procedure to identify testers top-ranked 'NASPOT 7' as a dual tester for both traits. Besides this parent, 'Ejumula' and 'NASPOT 10 O' for rytha, and 'NASPOT 1', 'NK259L', 'SPK004', and 'NASPOT 11' for vir2 are particularly suitable as respective single-trait testers. Testers are important in many plant breeding programs to enhance efficiency of RRS, and thus other crop species might benefit from the strategy and methods applied herein
Poverty and yield effects of CGIAR maize varieties in smallholder farming systems of Zambia
No full textImproved germplasm is a recognized adaptation strategy to climate change. We assessed the adoption, and impacts of CGIAR maize varieties on livelihoods in Zambia using fixed effects regression and a difference-in-differences framework. Three-waves of nationally representative panel data indicate that 24% of smallholders used CGIAR germplasm on about 225,000 hectares in 2019. Relative to other non-CGIAR maize varieties, the use of CGIAR maize varieties was associated with 26–35% yield increase, and 2–10% reduction in the depth of poverty on average. Thus, while improved varieties can increase crop productivity effectively, they are not substitutes for broad-based poverty reduction strategies.151-16