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.

KEY MESSAGE: 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.

Physicochemical Properties and Effect of Processing Methods on Mineral Composition and Antinutritional Factors of Improved Chickpea (Cicer arietinum L.) Varieties Grown in Ethiopia.

Chickpea (Cicer arietinum L.) is an important pulse crop grown and consumed all over the world because it is a good source of carbohydrates and protein. However, presence of antinutritional components restricts its use by interfering with digestion of macronutrients during consumption. Therefore, the objective of this study was to evaluate physicochemical properties and effect of processing methods on antinutritional factors and mineral composition of improved chickpea varieties (Natoli of Desi and Arerti of Kabuli) grown in Ethiopia. The experiment was factorial with complete randomized design. The result indicated that physicochemical properties such as seed mass, seed density, hydration capacity, swelling capacity, unhydrated seeds, and cooking time of Arerti and Natoli chickpeas had 260.69 and 280.65 g/1000 seeds, 3.48 and 3.61g/ml, 1.07 and 1.03 g/g, 2.12 and 1.94ml/g, 1.64 and 14.75%, and 21.00 and 246.33 min, respectively. After processing, Zn, Fe, and Ca contents of improved chickpea varieties had 4.48 to 5.85mg/kg, 8.52 to 10.17mg/kg, and 536.56 to 1035mg/kg, respectively. The antinutritional factors, tannin and phytic acid, in the raw chickpeas were reduced to 25 to 82.25% and 5.89 to 57.35%, respectively. The results of the current study showed that Arerti of Kabuli variety showed low antinutritional factors and better physicochemical properties, specifically low cooking time, than Natoli of Desi variety. All processing methods were effective in reduction of antinutritional factors; however, boiling was found to be the best for reduction of antinutritional factors.

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.

Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits.

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

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, ß-N-oxalyl-α,ß-diamiono propionic acid (ß-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 ß-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 ß-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 ß-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.

Correction: Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches.

[This corrects the article DOI: 10.1371/journal.pone.0096758.].

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.

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.

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.

Climatic, edaphic and altitudinal factors affecting yield and toxicity of Lathyrus sativus grown at five locations in Ethiopia.

A 2 years (2005-2006) data analysis based on agronomic, qualitative, climatic and edaphic factors was carried out using 10 grass pea (Lathyrus sativus L.) genotypes grown at five eco-divergent locations (Alem Tena, Debre Zeit, Denbi, Akaki, Chefe Donsa) in Ethiopia. Crop yield showed considerable variability among locations, years and genotypes. Path coefficient analysis indicated that rainfall and days to maturity have a large positive influence on yield. High level of micronutrients Mn(2+) and S(2-) negatively affected yield. Path analysis revealed that Zn(2+)/P, days to maturity, yield and K(+) were dominant variables affecting the response variable ß-ODAP (ß-N-oxalyl-L-α,ß-diaminopropionic acid), the neuro-excitatory amino acid in grass pea seeds considered as the cause of neurolathyrism. Linear correlation analysis between ß-ODAP and the 35 factors considered showed that ß-ODAP level was positively correlated (r > 0.70) with K(+) and sunshine hours (ssh) and negatively correlated (r < 0.70) with soil pH, days to maturity and yield. The strongest correlation of ssh with ß-ODAP level was found during the phase of crop maturity. Our results suggest that ß-ODAP biosynthesis and its response to environmental stress are maximized during the post-anthesis stage.

Effect of methionine supplement on physical responses and neurological symptoms in broiler chicks fed grass pea (Lathyrus sativus)-based starter ration.

Starter feeding experiments of broiler chicks with raw grass pea (Lathyrus sativus L.) supplemented with different levels of DL-methionine were undertaken for 4 weeks to assess the toxicity of grass pea-based feed and to correlate it with neurological symptoms. Four hundred fifty day-old broiler chicks were divided into two groups and were given formulations containing 35% (ration I) or 98.5% (ration II) grass pea, respectively. Each ration included controls and treatments with added methionine of four different concentrations. Feed intake, weight gain and feed conversion efficiency (FCE) were much higher in ration I than in ration II and these parameters significantly improved by addition of methionine in both rations. Significant increase of neurological signs with higher grass pea intake and significant reduction of acute neurological signs with addition of methionine were observed. Tolerance for grass pea was enhanced with increasing methionine in the diet and with age. Despite a similarity in the initial intake, a significant (p0.05) increase in the final feed intake by the chicks with methionine addition was found in both rations. These results suggest that methionine can improve a grass pea-based diet for broiler chicks and especially can protect young chicks from neurological symptoms.

The contents of the neuro-excitatory amino acid ß-ODAP (ß-N-oxalyl-l-α,ß-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 ß-ODAP (ß-N-oxalyl-l-α,ß-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.