A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.     

Smallholder rubber and swidden agriculture in Borneo: A sustainable adaptation to the ecology and economy of the tropical forest

This is a study of the role of Para rubber cultivation in a system of swidden agriculture in Indonesian Borneo. Such smallholdings produce most of Indonesia’s rubber, which is the country’s largest agricultural generator of foreign exchange. Rubber integrates well into Bornean systems of swidden agriculture: the comparative ecology and economy of Para rubber and upland swidden rice result in minimal competition in the use of land and labor — and even in mutual enhancement — between the two systems. Rubber occupies a distinct niche in the farm economy: it meets the need for market goods, while the swiddens meet subsistence needs. The intensity of production on these smallholdings is, as a result, characteristically low (and may even vary inversely with market prices). This reflects the independence of these smallholders from external economic and political influences, which has been the key to their historical success. The special virtues of such “composite systems” merit greater attention by development planners. Penilitian ini mempelajari peranan karet rakyat sebagai pasangan bagi sistem perladangan di Kalimantan-Indonesia. Perkebunan karet rakyat merupakan penghasil utama karet Indonesia, yang merupakan penyumbang pertanian terbesar bagi devisa negara. Karet rakyat membaur dengan baik dalam sistem perladangan di Kalimantan: pembandingan ekologi dan ekonomi antara karet rakyat dan sistem perladangan menunjukkan persaingan yang minimum dalam pemakaian lahan dan tenaga kerja—dan bahkan saling menguntungkan—antara kedua sistem tersebut. Karet rakyat menempati kedudukan yang penting dalam ekonomi usaha para peladang: yaitu memenuhi kebutuhan barang-barang pasar, sedangkan sistem perladangan memenuhi kebutuhan pokok hidup. Intensitas produksi perkebunan karet rakyat oleh karena itu, brasanya agak rendah (yang kadang-kadang berbeda berbalikan dengan harga pasar). Hal ini menggambarkan ketidak-bergantungan petani karet pada pengaruh-pengaruh ekonomi dan politik dari luar, dan ini merupakan kunci sukses mereka. Hal-hal khususyang menguntungkan dari sistem terpadu inipatut mendapatkanperhatian yang lebih besar dari perencana-perencana pembangunan.     

Bio-economic and operational feasibility of introducing oestrus synchronization and artificial insemination in simulated smallholder sheep breeding programmes

Low selection intensity due to few selection candidates available at any one time due to thinly spread year-round lambings in villages and prohibitively large nucleus requirements to provide sufficient improved rams to the production tier are the major challenges for designing effective village-based and central nucleus-based breeding programmes, respectively, for smallholder sheep farmers. To tackle these challenges, we used deterministic simulation to design three schemes in village-based programmes introducing hormonal oestrus synchronization (natural oestrus (VNE), single oestrus synchronization (VSE1) and double oestrus synchronization (VSE2)) and three schemes in central nucleus programme introducing artificial insemination (AI) (natural mating with nucleus sizes of 5% (CNM1) and 1% (CNM2) of the total ewe population and natural mating in breeding tier and AI in production tier (CAI)). The schemes were evaluated for their bio-economic and operational feasibility, taking Bonga sheep of Ethiopia as a case study. The selection intensities achieved in VNE, VSE1 and VSE2 were 2.0, 2.3 and 2.4, respectively, for selecting rams for the breeding tier and 0.0, 0.8 and 1.0, respectively, for the production tier. The profits per ewe per year from VNE, VSE1 and VSE2 were Birr 12.2, 21.7 and 24.5, but the profit from VNE for the production tier was zero. CAI generated more genetic gains in the breeding objective (Birr 4.8) than CNM1 (Birr 2.5) and CNM2 (Birr 0.0) in the production tier. However, CAI was less profitable than CNM1 and CNM2. In conclusion, hormonal oestrus synchronization was found to be a feasible technological aide to accelerate genetic progress in village-based programmes. CNM1 and CNM2 could not be recommended as CNM1 requires large nucleus of 10 325 ewes and CNM2 results in zero genetic gain in the production tier. CAI could overcome the challenge in central nucleus programmes, namely unaffordable large nucleus, but the scheme needs to be subsidized by the public sector to be economically feasible for farmers.     

Effects of cultivation practice on floristic and flowering diversity of spontaneously growing plant species on arable fields

In the past, the floristic diversity of arable fields has been described in terms of species diversity (SD) and their degree of coverage (C), but never in combination with the recording of the actually flowered species (FS) and their flowering intensity (FI) to striking differences in the cultivation methods on arable land. In relation to SD and C, however, FS and FI may provide important additional information on the functional biodiversity of fields. The aim was therefore to investigate the effects of (a) conventional, (b) organic, and (c) smallholder (never application of herbicides) on the floristic diversity. Using a region in Germany, we investigated SD, C, FS, and FI synchronously in (a), (b), and (c), by 356 vegetation surveys (5 × 5 m plots) conducted in spring and summer in 2019 in winter cereals. Statistical tests were used to analyze the differences between (a), (b), and (c). The medians were used to compare the floristic diversity of (a), (b), and (c) and finally relationships of FS and FI to SD were analyzed in relation to the cultivation methods. Significant differences in SD, C, FS, and FI were found between the (a), (b), and (c) in spring and summer characterized by sharp declines from (c) to (b) to (a). A drastic reduction in floristic diversity from (c) 100 to (b) 52 to (a) 3 was determined. Plants in flower (FS, FI) were very poorly in (a), moderately well to well in (b), and well to very well represented in (c). (C) to (a) was characterized by a sharp decline and from (a) to (b) by sharp increase in floristic diversity. With current acreage proportions of (a) in mind, this would affect, about one third of land area in Germany, associated with a drastic reduction in functional biodiversity for insects.     

The genomic and bioclimatic characterization of Ethiopian barley (Hordeum vulgare L.) unveils challenges and opportunities to adapt to a changing climate

The climate crisis is impacting agroecosystems and threatening food security of millions of smallholder farmers. Understanding the potential for current and future climatic adaptation of local crop agrobiodiversity may guide breeding efforts and support resilience of agriculture. Here, we combine a genomic and climatic characterization of a large collection of traditional barley varieties from Ethiopia, a staple for local smallholder farmers cropping in challenging environments. We find that the genomic diversity of barley landraces can be partially traced back to geographic and environmental diversity of the landscape. We employ a machine learning approach to model Ethiopian barley adaptation to current climate and to identify areas where its existing diversity may not be well adapted in future climate scenarios. We use this information to identify optimal trajectories of assisted migration compensating to detrimental effects of climate change, finding that Ethiopian barley diversity bears opportunities for adaptation to the climate crisis. We then characterize phenology traits in the collection in two common garden experiments in Ethiopia, using genome-wide association approaches to identify genomic loci associated with timing of flowering and maturity of the spike. We combine this information with genotype–environment associations finding that loci involved in flowering time may also explain environmental adaptation. Our data show that integrated genomic, climatic, and phenotypic characterizations of agrobiodiversity may provide breeding with actionable information to improve local adaptation in smallholder farming systems.     

Efficiency of selection for body weight in a cooperative village breeding program of Menz sheep under smallholder farming system

We evaluated the efficiency of selection for body weight in a cooperative village breeding program for Menz sheep of Ethiopia under smallholder farming system. The design of the program involved organizing villagers in a cooperative breeding group to implement selective breeding of their sheep. The program was jump-started through a one-time provision of elite rams from a central nucleus flock, but subsequent replacement rams were selected from within the village flocks. We also evaluated body weight trends in a village where cooperative breeding was not implemented and individual farmers managed their flocks under traditional breeding practices. Under traditional breeding practices, genetic progress over 8 years either stagnated or declined in all the weights recorded. In the cooperative villages, selection differentials of 2.44 and 2.45 kg were achieved in 2010 and 2011 selection seasons, respectively. Birth weight, 3-month weight and 6-month weight increased, respectively, by 0.49, 2.29 and 2.46 kg in the third-generation lambs over the base generation. Improved rams supplied from the central nucleus flock gave an initial genetic lift of 14.4% in the 6-month weight. This was higher than the gain achieved from selection in the village flocks, which was 5.2%. Our results showed that village-based genetic improvement in body weights under smallholder conditions could be feasible if appropriate designs are adopted and that commencing with elite central nucleus rams help jump-start village-based programs.     

Intensification of dairy production can increase the GHG mitigation potential of the land use sector in East Africa

Sub‐Saharan Africa (SSA) could face food shortages in the future because of its growing population. Agricultural expansion causes forest degradation in SSA through livestock grazing, reducing forest carbon (C) sinks and increasing greenhouse gas (GHG) emissions. Therefore, intensification should produce more food while reducing pressure on forests. This study assessed the potential for the dairy sector in Kenya to contribute to low‐emissions development by exploring three feeding scenarios. The analyses used empirical spatially explicit data, and a simulation model to quantify milk production, agricultural emissions and forest C loss due to grazing. The scenarios explored improvements in forage quality (Fo), feed conservation (Fe) and concentrate supplementation (Co): FoCo fed high‐quality Napier grass (Pennisetum purpureum), FeCo supplemented maize silage and FoFeCo a combination of Napier, silage and concentrates. Land shortages and forest C loss due to grazing were quantified with land requirements and feed availability around forests. All scenarios increased milk yields by 44%–51%, FoCo reduced GHG emission intensity from 2.4 ± 0.1 to 1.6 ± 0.1 kg CO₂eq per kg milk, FeCo reduced it to 2.2 ± 0.1, whereas FoFeCo increased it to 2.7 ± 0.2 kg CO₂eq per kg milk because of land use change emissions. Closing the yield gap of maize by increasing N fertilizer use reduced emission intensities by 17% due to reduced emissions from conversion of grazing land. FoCo was the only scenario that mitigated agricultural and forest emissions by reducing emission intensity by 33% and overall emissions by 2.5% showing that intensification of dairy in a low‐income country can increase milk yields without increasing emissions. There are, however, risks of C leakage if agricultural and forest policies are not aligned leading to loss of forest to produce concentrates. This approach will aid the assessment of the climate‐smartness of livestock production practices at the national level in East Africa.     

Meta-analysis of the effects of on-farm management strategies on milk yields of dairy cattle on smallholder farms in the Tropics

Although East Africa is home to one of the most advanced dairy industries in Sub-Saharan Africa, regional annual milk production is insufficient to meet the demand. The challenge of increasing milk yields (MYs) among smallholder dairy cattle farmers (SDCFs) has received considerable attention and resulted in the introduction of various dairy management strategies (DMSs). Despite adoption of these DMSs, MYs remain low on-farm and there is a large discrepancy in the efficacy of DMSs across different farms. Therefore, the present study sought to: (1) identify on-farm DMSs employed by East African SDCFs to increase MYs and (2) summarize existing literature to quantify the expected MY changes associated with these identified DMSs. Data were collected through a comprehensive literature review and in-depth semi-structured interviews with 10 experts from the East African dairy sector. Meta-analysis of the literature review data was performed by deriving four multivariate regression models (i.e. models 1 to 4) that related DMSs to expected MYs. Each model differed in the weighting strategy used (e.g. number of observations and inverse of the standard errors) and the preferred model was selected based on the root estimated error variance and concordance correlation coefficient. Nine DMSs were identified, of which only adoption of improved cattle breeds and improved feeding (i.e. increasing diet quality and quantity) consistently and significantly (P < 0.05) increased daily MYs across the available studies. Improved breeds alongside adequate feeding explained ≤50% of the daily MYs observed in the metadata while improved feeding explained ≤30% of the daily MYs observed across the different models. Conversely, calf suckling significantly (P < 0.05) reduced MYs according to model 2. Other variables including days in milk, trial length and maximum ambient temperature (used as a proxy for heat stress) contributed significantly to decreasing MYs. These variables may explain some of the heterogeneity in MY responses to DMSs reported in the literature. Our results suggest that using improved cattle breeds alongside improved feeding is the most reliable strategy to increase MYs on-farm in East Africa. Nevertheless, these DMSs should not be considered as standalone solutions but as a pool of options that should be combined depending on the resources available to the farmer to achieve a balance between using dairy cattle genetics, proper husbandry and feeding to secure higher MYs.     

Effects of Organic Resource Quality on Soil Profile N Dynamics and Maize Yields on Sandy Soils in Zimbabwe

Optimising the use efficiency of nitrogen (N) derived from different quality organic resources and mineral fertilizers on sandy soils with <100 g clay kg⁻¹ is a major challenge for smallholder farmers in Southern Africa. The dominant sandy soils have a poor capacity to store and supply crop nutrients due to low organic matter contents and inherent infertility. A study was conducted in Zimbabwe to determine the differential N supply effects of different quality and quantities of organic nutrient sources on maize productivity. Crotalaria juncea L., Calliandra calothyrsus Meissn., cattle manure, maize (Zea mays L.) stover and Pinus patula Schiede & Schltdl. & Cham. sawdust which represented high to low quality materials respectively, were each incorporated into soil at 1.2 and 4 t C ha⁻¹ at Makoholi Experiment Station (rainfall: 450–650 mm yr⁻¹) and tested against a sole mineral N fertilizer and control treatments. In a separate experiment conducted in farmers’ fields under different rainfall zones of Zimuto (450–650 mm yr⁻¹), Chinyika (650–750 mm yr⁻¹) and Chikwaka (>750 mm yr⁻¹), commonly available organic materials, including manure and composted miombo leaf litter, applied in varying amounts by farmers were evaluated. Nitrogen release patterns were consistent with differences in resource quality. At 3 weeks after incorporation into soil at the onset of the rains, C. juncea and C. calothyrsus had released as high as 24% and 13% of added N respectively, compared with no more than 5–6% for the rest of the amended treatments. Most of the N released was lost through leaching as evidenced by progressive movement of NO₃⁻-N bulges beyond maize rooting depth following major rainfall events. Maize yields were significantly related to the size of profile mineral N fluxes, with the best linear relationship (R² = 0.86) obtained with N available in the top 30 cm of soil at maize flowering. High grain yields of ~3 t ha⁻¹ were only achieved with C. juncea applied at 4 t C ha⁻¹, which also had highest NO₃⁻-N leaching losses. Conversely, the same application rate increased N immobilization by 30% and 42% under maize stover and sawdust, respectively, relative to the control. Results from farmers’ fields showed that organic resources traditionally used on smallholder farms are invariably of low quality relative to C. juncea and C. calothyrsus. However, they exhibited shorter N immobilization effects than was shown for maize stover and sawdust at Makoholi, suggesting that pre-application treatments, such as composting, employed by farmers enhance seasonal N benefits from these materials. Maize yields increased linearly with total N added in these resources in combination with N fertilizer, justifying the high organic matter loading strategy (e.g. >20 t ha⁻¹ for manure, fresh litter and composted litter) used by farmers who often achieve high crop yields on such coarse sandy soils in Zimbabwe.     

Applying Industrial Symbiosis to Smallholder Farms

The study of industrial symbiosis (IS) has largely focused on the exchange of energy and materials among industrial processes in an effort to increase value and reduce environmental impact. Agricultural systems, particularly those located in developing countries, can benefit from the principles of IS. Relatively few studies have analyzed the potential benefits of integrated material and energy flows in smallholder farming, even though these systems are considered essential to the world's food supply and poverty reduction. Although the concepts can be applied to virtually any system, the study of industrial symbiosis has traditionally focused on industrialized systems in developed countries. The research presented here applies the principles of IS to smallholder farms using optimization techniques to maximize farm output while minimizing wastes. Our research links IS to the growing field of integrated farming research (IFR), which seeks to create new technologies that increase the production of farms by viewing the farm as a system. Bridging these fields enriches the potential for robust research outcomes in both areas and fills a current knowledge gap. IS benefits from exploring new applications and increasing its penetration into the developing world. IFR benefits from established IS tools to create alternate pathways for increased output based on symbiotic relationships. A small farming system in Liberia, West Africa, is used as a case study. System integration of individual unit processes shows increased productivity and decreased waste. The results of this analysis indicate that there are unrealized opportunities for IS in developing countries, and integration of IS techniques into smallholder farming operations has the potential for impacting sustainable development.