Participatory variety evaluation and selection of chickpea (Cicer arietinum L.) varieties; an underpinning to novel technology uptake in northwestern Ethiopia

The productivity and production of chickpeas can be improved by using access-improved varieties that are suitable for the specific agroecology. However, the foundation for adopting new technology is participatory variety selection (PVS). Therefore, this study aimed to identify the best adaptively improved chickpea varieties in northwestern Ethiopia based on the preferences of farmers in Adet and Fogera Districts. The experiment consisted of ten improved chickpea varieties (Desi and Kabuli) that were evaluated in three replications using the mother baby trail approach, including on-station and on-farm evaluations. According to this trail, the highest grain yield among different types of chickpeas was observed in the varieties Teketay (2327.8 kg/ha), Dalota (2175.9 kg/ha), and Geletu (2123.6 kg/ha). Among the Kabuli types, Koka (2813.2 kg/ha) and Dhera (2325.7 kg/ha) showed the highest mean values of grain yield. At Adet location, the varieties Teketay (2772.2 kg/ha), Dalota (2459.7 kg/ha), and Geletu (2270.8 kg/ha) produced the highest grain yield. Similarly, Koka (3195.8 kg/ha), Dhera (2604.2 kg/ha), and Ejere (2601.4 kg/ha) were the top-yielding Kabuli chickpea varieties. Farmers from Adet location in Senkengha Kebele selected three Desi and three Kabuli chickpea varieties, namely Geletu, Teketay, and Dalota, in that order, as well as Koka, Hora, and Ejere. Meanwhile, farmers in Mousobo Kebele identified Koka, Dhera, and Hora from the Kabuli type as the best varieties. The varieties Geletu (1976.4 kg/ha), Dalota (1891.9 kg/ha), and Teketay (1883.3 kg/ha) had the highest mean grain yield at Fogera location. Similarly, in the Kabuli chickpea varieties, the highest mean value of grain yield was obtained from Koka (2430.6 kg/ha) followed by Hora (2097.2 kg/ha), and Dhera (2047.2 kg/ha). Farmers have chosen three of the best Desi and Kabuli chickpea varieties, i.e Geletu, Teketay, and Dalota, and Local check (Shasho) followed by Koka and Ejere at Fogera location, Geina Kebele in that order. In conclusion, the adoption and dissemination of new improved varieties for the new environment can assist the producers such as the farmers for effective chickpea production. This leads to sustainable self-sufficiency of food at the household and country level.

Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris

Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security. Fusarium oxysporum is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.

Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants

The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil-based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low-income countries. The rhizobox is large enough (approximately 6000 cm² of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low- and middle-income countries to enhance crop yields and climate resilience sustainably.

Integrating genomics for chickpea improvement: achievements and opportunities

Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.

Reducing anti-nutritional factor and enhancing yield with advancing time of planting and zinc application in grasspea in Ethiopia

BACKGROUND

Grasspea (Lathyrus sativus L.) is an important pulse crop for food, feed and sustainable crop production systems in Ethiopia. Despite its advantages in nutrition and adaptability to harsh climate and low fertile soil, it contains a neurotoxin, β-N-oxalyl-α,β-diamiono propionic acid (β-ODAP), which paralyses the lower limbs and is affected by genotypic and agronomic factors. To determine the effect of zinc application and planting date on yield and β-ODAP content of two genotypes, experiments were conducted in two regions of Ethiopia.

RESULTS

The main effects of variety, sowing date and zinc and their interactions were significant (P < 0.001) for β-ODAP and seed yield, which had a linear relationship with zinc. For the improved grasspea variety, an application of 20 kg ha^-1 zinc showed a reduction of β-ODAP from 0.15% to 0.088% at Debre Zeit and 0.14% to 0.08% at Sheno and increased its yield from 841 kg ha^-1 to 2260 kg ha^-1 at Debre Zeit and from 715 to 1835 kg ha^-1 at Sheno. Early sowing showed a reduction in ODAP content in relation to the late sowing.

CONCLUSION

An application of Zn beyond even 20 kg ha^-1 with an early sowing is recommended for the improved variety. © 2017 Society of Chemical Industry.

Genomics-assisted breeding for drought tolerance in chickpea

Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.

Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1-7 seasons and 1-3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.

Studies on neurolathyrism in Ethiopia: dietary habits, perception of risks and prevention

This study describes the correlation of traditional perceptions and dietary habits with the incidence of neurolathyrism to propose preventive measures. Therefore, 118 households of South Wollo and North Gondar (Amhara Regional State, Ethiopia), of which one third had at least one neurolathyrism affected member, were interviewed. Most of the affected families in this study had one neurolathyrism victim, being predominantly male and of younger age. The incidence among youngsters (boys and girls) was significantly correlated with the consumption of green unripe seeds (eshet), confirming this as a risk factor for developing neurolathyrism. The consumption of other popular grass pea preparations was not age related. Neurolathyrism patients did not attempt any medication as most people knew that neurolathyrism is incurable, but the consumption of grass pea was abandoned after developing the disease. The minority 'Woito' tribe was virtually unaffected. They were the only people reporting to consume fish which is rich in amino acids such as methionine and using metallic kitchen utensils in addition to clay pots. This observation points to the correlation between low neurolathyrism incidence and a better balanced diet as well as metallic kitchen utensils, suggesting a new approach for neurolathyrism prevention.

The contents of the neuro-excitatory amino acid β-ODAP (β-N-oxalyl-l-α,β-diaminopropionic acid), and other free and protein amino acids in the seeds of different genotypes of grass pea (Lathyrus sativus L.)

The free and protein amino acids of nine different genotypes of grass pea (Lathyrus sativus L.) seeds were analysed by HPLC with pre-column PITC (phenyl isothiocyanate) derivatisation. Among the free amino acids, homoarginine was quantitatively the most important (up to 0.8% seed weight) and stable while the neuro-excitatory amino acid β-ODAP (β-N-oxalyl-l-α,β-diaminopropionic acid) showed highest variation (0.02-0.54%) in the nine genotypes examined. Among protein amino acids, glutamic acid was quantitatively most significant, followed by aspartic acid, arginine, leucine, lysine and proline. The sulphur amino acid, methionine, showed the lowest concentration in all the L. sativus genotypes, and also in lentil (Lens culinaris) and in soybean (Glycine max) seeds analysed at the same time.