Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Meta QTL analysis for dissecting abiotic stress tolerance in chickpea

BACKGROUND

Chickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea.

RESULTS

A meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc. CONCLUSION: The results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.

Impact of low light intensity on biomass partitioning and genetic diversity in a chickpea mapping population

With recent climatic changes, the reduced access to solar radiation has become an emerging threat to chickpeas' drought tolerance capacity under rainfed conditions. This study was conducted to assess, and understand the effects of reduced light intensity and quality on plant morphology, root development, and identifying resistant sources from a Sonali/PBA Slasher mapping population. We evaluated 180 genotypes, including recombinant inbred lines (RILs), parents, and commercial checks, using a split-block design with natural and low light treatments. Low light conditions, created by covering one of the two benches inside two growth chambers with a mosquito net, reduced natural light availability by approximately 70%. Light measurements encompassed photosynthetic photon flux density, as well as red, and far-red light readings taken at various stages of the experiment. The data, collected from plumule emergence to anthesis initiation, encompassed various indices relevant to root, shoot, and carbon gain (biomass). Statistical analysis examined variance, treatment effects, heritability, correlations, and principal components (PCs). Results demonstrated significant reductions in root biomass, shoot biomass, root/shoot ratio, and plant total dry biomass under suboptimal light conditions by 52.8%, 28.2%, 36.3%, and 38.4%, respectively. Plants also exhibited delayed progress, taking 9.2% longer to produce their first floral buds, and 19.2% longer to commence anthesis, accompanied by a 33.4% increase in internodal lengths. A significant genotype-by-environment interaction highlighted differing genotypic responses, particularly in traits with high heritability (> 77.0%), such as days to anthesis, days to first floral bud, plant height, and nodes per plant. These traits showed significant associations with drought tolerance indicators, like root, shoot, and plant total dry biomass. Genetic diversity, as depicted in a genotype-by-trait biplot, revealed contributions to PC1 and PC2 coefficients, allowing discrimination of low-light-tolerant RILs, such as 1_52, 1_73, 1_64, 1_245, 1_103, 1_248, and 1_269, with valuable variations in traits of interest. These RILs could be used to breed desirable chickpea cultivars for sustainable production under water-limited conditions. This study concludes that low light stress disrupts the balance between root and shoot morphology, diverting photosynthates to vegetative structures at the expense of root development. Our findings contribute to a better understanding of biomass partitioning under limited-light conditions, and inform breeding strategies for improved drought tolerance in chickpeas.

Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species

Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.

Functional allele of a MATE gene selected during domestication modulates seed color in chickpea

Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.

SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.)

Genetic diversity and marker-trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.

Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.)

Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.

Disentangling potential genotypes for macro and micro nutrients and polymorphic markers in Chickpea

The present investigation was conducted to assess the nutritional diverseness and identify novel genetic resources to be utilized in chickpea breeding for macro and micro nutrients. The plants were grown in randomized block design. Nutritional and phytochemical properties of nine chickpea genotypes were estimated. The EST sequences from NCBI database were downloaded in FASTA format, clustered into contigs using CAP3, mined for novel SSRs using TROLL analysis and primer pairs were designed using Primer 3 software. Jaccard's similarity coefficients were used to compare the nutritional and molecular indexes followed by dendrograms construction employing UPGMA approach. The genotypes PUSA-1103, K-850, PUSA-1108, PUSA-1053 and the EST-SSR markers including the 5 newly designed namely ICCeM0012, ICCeM0049, ICCeM0067, ICCeM0070, ICCeM0078, SVP55, SVP95, SVP96, SVP146, and SVP217 were found as potential donor/marker resources for the macro-micro nutrients. The genotypes differed (p < 0.05) for nutritional properties. Amongst newly designed primers, 6 were found polymorphic with median PIC (0.46). The alleles per primer ranged 1 to 8. Cluster analysis based on nutritional and molecular diversities partially matched to each other in principle. The identified novel genetic resources may be used to widen the germplasm base, prepare maintainable catalogue and identify systematic blueprints for future chickpea breeding strategies targeting macro-micro nutrients.

Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data from Cicer arietinum L. and C. reticulatum Ladiz. A total of 35,329 InDels were obtained in C. arietinum, whereas 44,331 InDels in C. reticulatum. 3387 InDels with 2 bp length were detected in C. arietinum, there were 4704 in C. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes including C. arietinum, C. reticulatum, C. echinospermum P.H. Davis, C. anatolicum Alef., C. canariense A. Santos & G.P. Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum Steph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross between C. arietinum and C. reticulatum. Chi-square (χ²) test revealed an expected 1:1 segregation ratio in the population. These results demonstrated the success of SSR identification and marker development for chickpea with the use of WGRS data. The newly developed 58 SSR markers are expected to be useful for chickpea breeders.

Underutilized legumes: nutrient status and advanced breeding approaches for qualitative and quantitative enhancement

Underutilized/orphan legumes provide food and nutritional security to resource-poor rural populations during periods of drought and extreme hunger, thus, saving millions of lives. The Leguminaceae, which is the third largest flowering plant family, has approximately 650 genera and 20,000 species and are distributed globally. There are various protein-rich accessible and edible legumes, such as soybean, cowpea, and others; nevertheless, their consumption rate is far higher than production, owing to ever-increasing demand. The growing global urge to switch from an animal-based protein diet to a vegetarian-based protein diet has also accelerated their demand. In this context, underutilized legumes offer significant potential for food security, nutritional requirements, and agricultural development. Many of the known legumes like Mucuna spp., Canavalia spp., Sesbania spp., Phaseolus spp., and others are reported to contain comparable amounts of protein, essential amino acids, polyunsaturated fatty acids (PUFAs), dietary fiber, essential minerals and vitamins along with other bioactive compounds. Keeping this in mind, the current review focuses on the potential of discovering underutilized legumes as a source of food, feed and pharmaceutically valuable chemicals, in order to provide baseline data for addressing malnutrition-related problems and sustaining pulse needs across the globe. There is a scarcity of information about underutilized legumes and is restricted to specific geographical zones with local or traditional significance. Around 700 genera and 20,000 species remain for domestication, improvement, and mainstreaming. Significant efforts in research, breeding, and development are required to transform existing local landraces of carefully selected, promising crops into types with broad adaptability and economic viability. Different breeding efforts and the use of biotechnological methods such as micro-propagation, molecular markers research and genetic transformation for the development of underutilized crops are offered to popularize lesser-known legume crops and help farmers diversify their agricultural systems and boost their profitability.

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China

Background

Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.

Methods

Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.

Results

A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.

Solid Lipid Nanoparticles: Peculiar Strategy to Deliver Bio-Proactive Molecules

BACKGROUND

Novel Drug Delivery Systems (NDDS) provide numerous benefits compared to conventional dosage forms. Poor aqueous solubility, low bioavailability, frequent dosing, and particular hydrophilic lipophilic character of the drug are the biological factors associated with the traditional systems leading to the development of SLNs.

OBJECTIVE

For improving the solubility profile, enhancing the bioavailability, and attaining the best possible therapeutic effect of lipid inclined or aqueous inclined drug, formulating solid lipid nanoparticles is the best choice.

METHODS

Solid Lipid Nanoparticles (SLNs) have been projected as a colloidal carrier system with a size of 50-1,000 nm, collectively combining the benefits of other colloidal systems like liposomes, emulsions, etc., for delivering the drug at the target site. High absorption, high stability, and efficient drug packing enhance the pharmacokinetic and pharmacodynamic properties of the packed drug.

RESULT

Solid Lipid Nanoparticles can be developed in different dosage forms and administered via routes such as nasal, rectal, oral, topical, vaginal, ocular, and parenteral. They have higher physicochemical stability and the batch size can be easily scaled up at a low cost. Lipophilic as well as hydrophilic drugs can be easily incorporated into solid lipid nanoparticles.

CONCLUSION

In this manuscript, the authors have reviewed different aspects of solid lipid nanoparticles, major principles behind mechanism methods, recent patents, applications, and therapeutic potentials of solid lipid nanoparticles.

Molecular Breeding and Drought Tolerance in Chickpea

Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).

Chickpea (Cicer arietinum L.) Biology and Biotechnology: From Domestication to Biofortification and Biopharming

Chickpea (Cicer arietinum L.), the world's second most consumed legume crop, is cultivated in more than 50 countries around the world. It is a boon for diabetics and is an excellent source of important nutrients such as vitamins A, C, E, K, B1-B3, B5, B6, B9 and minerals (Fe, Zn, Mg and Ca) which all have beneficial effects on human health. By 2050, the world population can cross 9 billion, and in order to feed the teaming millions, chickpea production should also be increased, as it is a healthy alternative to wheat flour and a boon for diabetics. Moreover, it is an important legume that is crucial for food, nutrition, and health security and the livelihood of the small-scale farmers with poor resources, in developing countries. Although marvelous improvement has been made in the development of biotic and abiotic stress-resistant varieties, still there are many lacunae, and to fulfill that, the incorporation of genomic technologies in chickpea breeding (genomics-assisted breeding, high-throughput and precise-phenotyping and implementation of novel breeding strategies) will facilitate the researchers in developing high yielding, climate resilient, water use efficient, salt-tolerant, insect/pathogen resistant varieties, acceptable to farmers, consumers, and industries. This review focuses on the origin and distribution, nutritional profile, genomic studies, and recent updates on crop improvement strategies for combating abiotic and biotic stresses in chickpea.

Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea

Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.

Genome-wide association mapping of nutritional traits for designing superior chickpea varieties

Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56-24.64/100 g), β-Carotene (0.003-0.104 mg/100 g), calcium (60.69-176.55 mg/100 g), and folate (0.413-6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation-reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.

Genetic mapping of QTLs for drought tolerance in chickpea (Cicer arietinum L.)

Chickpea yield is severely affected by drought stress, which is a complex quantitative trait regulated by multiple small-effect genes. Identifying genomic regions associated with drought tolerance component traits may increase our understanding of drought tolerance mechanisms and assist in the development of drought-tolerant varieties. Here, a total of 187 F8 recombinant inbred lines (RILs) developed from an interspecific cross between drought-tolerant genotype GPF 2 (Cicer arietinum) and drought-sensitive accession ILWC 292 (C. reticulatum) were evaluated to identify quantitative trait loci (QTLs) associated with drought tolerance component traits. A total of 21 traits, including 12 morpho-physiological traits and nine root-related traits, were studied under rainfed and irrigated conditions. Composite interval mapping identified 31 QTLs at Ludhiana and 23 QTLs at Faridkot locations for morphological and physiological traits, and seven QTLs were identified for root-related traits. QTL analysis identified eight consensus QTLs for six traits and five QTL clusters containing QTLs for multiple traits on linkage groups CaLG04 and CaLG06. The identified major QTLs and genomic regions associated with drought tolerance component traits can be introgressed into elite cultivars using genomics-assisted breeding to enhance drought tolerance in chickpea.

Conventional and molecular breeding for disease resistance in chickpea: status and strategies

Chickpea (Cicer arietinum L.) is an important grain legume at the global level. Among different biotic stresses, diseases are the most important factor limiting its production, causing yield losses up to 100% in severe condition. The major diseases that adversely affect yield of chickpea include Fusarium wilt, Ascochyta blight and Botrytis gray mold. However, dry root rot, collar rot, Sclerotinia stem rot, rust, stunt disease and phyllody have been noted as emerging biotic threats to chickpea production in many production regions. Identification and incorporation of different morphological and biochemical traits are required through breeding to enhance genetic gain for disease resistance. In recent years, remarkable progress has been made in the development of trait-specific breeding lines, genetic and genomic resources in chickpea. Advances in genomics technologies have opened up new avenues to introgress genes from secondary and tertiary gene pools for improving disease resistance in chickpea. In this review, we have discussed important diseases, constraints and improvement strategies for enhancing disease resistance in chickpea.

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.

Defining the mutation sites in chickpea nodulation mutants PM233 and PM405

BACKGROUND

Like most legumes, chickpeas form specialized organs called root nodules. These nodules allow for a symbiotic relationship with rhizobium bacteria. The rhizobia provide fixed atmospheric nitrogen to the plant in a usable form. It is of both basic and practical interest to understand the host plant genetics of legume root nodulation. Chickpea lines PM233 and PM405, which harbor the mutationally identified nodulation genes rn1 and rn4, respectively, both display nodulation-deficient phenotypes. Previous investigators identified the rn1 mutation with the chickpea homolog of Medicago truncatula nodulation gene NSP2, but were unable to define the mutant rn1 allele. We used Illumina and Nanopore sequencing reads to attempt to identify and characterize candidate mutation sites responsible for the PM233 and PM405 phenotypes.

RESULTS

We aligned Illumina reads to the available desi chickpea reference genome, and did a de novo contig assembly of Nanopore reads. In mutant PM233, the Nanopore contigs allowed us to identify the breakpoints of a ~ 35 kb deleted region containing the CaNSP2 gene, the Medicago truncatula homolog of which is involved in nodulation. In mutant PM405, we performed variant calling in read alignments and identified 10 candidate mutations. Genotyping of a segregating progeny population narrowed that pool down to a single candidate gene which displayed homology to M. truncatula nodulation gene NIN.

CONCLUSIONS

We have characterized the nodulation mutation sites in chickpea mutants PM233 and PM405. In mutant PM233, the rn1 mutation was shown to be due to deletion of the entire CaNSP2 nodulation gene, while in mutant PM405 the rn4 mutation was due to a single base deletion resulting in a frameshift mutation between the predicted RWP-RK and PB1 domains of the NIN nodulation gene. Critical to characterization of the rn1 allele was the generation of Nanopore contigs for mutant PM233 and its wild type parent ICC 640, without which the deletional boundaries could not be defined. Our results suggest that efforts of prior investigators were hampered by genomic misassemblies in the CaNSP2 region of both the desi and kabuli reference genomes.

Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Vigna umbellata)

Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development-related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development-related traits in ricebeans. A total of 51 genes encoding SCF TIR1/AFB , Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean-derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.

Chickpea tolerance to temperature stress: Status and opportunity for improvement

Chickpea is a globally important commercial crop and a key source of protein for vegetarian populations. Though chickpea was domesticated at least 3000 years ago, research into abiotic stress tolerance has been limited compared to cereal crops such as wheat. This review investigates the impacts of heat stress on chickpea, focusing on reproductive development. The fertilisation process is particularly sensitive to environmental stress, such as drought and heat that can reduce yields by up to 70%. Current research has largely focused on breeding cultivars that reach maturity faster to avoid stress rather than true thermotolerance and little is known of the impact of heat on cellular processes. This review suggests that there is ample variation within the chickpea gene pool for selective breeding to achieve improved abiotic stress tolerance. Rates of genetic progress will improve once key QTL are identified and the link between thermotolerance and pollen viability confirmed. Other benefits may arise from better understanding of heat shock proteins and molecular chaperones and their role in the protection of reproductive processes.

Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

Unraveling genetics of semi-determinacy and identification of markers for indeterminate stem growth habit in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is predominantly an indeterminate plant and tends to generate vegetative growth when the ambient is conducive for soil moisture, temperature and certain other environmental conditions. The semi-determinate (SDT) types are comparatively early, resistant to lodging and found to be similar in their yield potential to indeterminate (IDT) lines. Indeterminate and semi-determinate genotypes are found to be similar during early stage, which makes it difficult to distinguish between them. Thus, there is a need to identify molecular markers linked either to indeterminate or semi-determinate plant types. The present study was carried out to study the genetics of semi-determinacy and identify molecular markers linked to stem growth habit. The study was undertaken in the cross involving BG 362(IDT) × BG 3078-1(SDT). All F₁ plants were indeterminate, which indicates that indeterminate stem type is dominant over semi-determinate. In further advancement to F₂ generation, F₂ plants are segregated in the ratio of 3(Indeterminate): 1(Semi-determinate) that indicates that the IDT and SDT parents which are involved in the cross differed for a single gene. The segregation pattern observed in F₂ is confirmed in F₃ generation. The parental polymorphic survey was undertaken for molecular analysis using total of 245 SSR markers, out of which 41 polymorphic markers were found to distinguish the parents and were utilized for bulked segregant analysis (BSA). The segregation pattern in F₂ indicates that the IDT (Indeterminate) and SDT (Semi-determinate) parents which are involved in the cross differed for single gene. The segregation pattern of F₂ and F₃ derived from the cross BG 362 (IDT) × BG 3078-1 (SDT) confirmed the genotypic structure of the newly found SDT genotype BG 3078-1 as dt1dt1Dt2Dt2. Three SSR markers TA42, Ca_GPSSR00560 and H3DO5 were found to be putatively linked to Dt1 locus regulating IDT stem growth habit. Our results indicate that the SSR markers identified for Dt1 locus helps to differentiate stem growth habit of chickpea in its early growth stage itself and can be efficiently utilized in Marker Assisted Selection (MAS) for changed plant type in chickpea.

Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292

Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.

Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions

Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.

Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

Chickpea-the second most important grain legume worldwide-is cultivated mainly on marginal soils. Phosphorus (P) deficiency often restricts chickpea yields. Understanding the genetics of traits encoding P-acquisition efficiency and P-use efficiency will help develop strategies to reduce P-fertilizer application. A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated proxy traits. Using three statistical models-a generalized linear model (GLM), a mixed linear model (MLM), and a fixed and random model circulating probability unification (FarmCPU) -10, 51, and 40 marker-trait associations (MTAs), respectively were identified. A single nucleotide polymorphism (SNP) locus (Ca1_12310101) on Ca1 associated with three traits, i.e., physiological P-use efficiency, shoot dry weight, and shoot P content was identified. Genes related to shoot P concentration (NAD kinase 2, dynamin-related protein 1C), physiological P-use efficiency (fasciclin-like arabinogalactan protein), specific root length (4-coumarate-CoA ligase 1) and manganese concentration in mature leaves (ABC1 family protein) were identified. The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.

Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea (Cicer arietinum L.) using genotyping by sequencing

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F₈ Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.

Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars

With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC₃ F₃ in Pusa 372; 20 BC₂ F₃ in Pusa 362, and 21 BC₃ F₃ in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.

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.

Gene-Based Marker to Differentiate Among B, A, and R Lines in Hybrid Production of Rapeseed Ogura System

Background:

In plant breeding program to produce hybrid varieties, pair of male sterile and restorer fertility lines are required. Differentiation of lines possessing restorer fertility allele from the lines lacking it remove the need for the progeny test, and thus reducing the time and the cost in the hybrid production procedure. Canola breeding program in Iran has concentrated toward production of domestic hybrid varieties, however, it suffers from lack of molecular information in restore fertility status of lines, and therefore it needs time and tedious activities.

Objectives:

To design gene-based markers for distinguishing R-, A- lines and hybrids in sunflower breeding programs.

Material and Methods:

Aligning sequences of locus responsible for male sterility and that of male fertility resulted in finding differences in the loci, which used to define two set of suitable primer pairs. Genomic DNA from 25 R-lines (23 inbred lines and two commercial lines), 9 A-lines (7 inbred lines and two commercial lines), one B-line and two commercial hybrids were extracted and used in PCR as template.

Results:

Using one-primer pairs, a band of nearly 1500 bp was amplified in restorer lines but not in A-, B- lines. Another primer pair used to distinguish hybrids (heterozygout) from restorer lines. Results of the report is predicted to be used in canola breeding for hybrid production.

Conclusions:

Although the molecular bases for the male sterility and fertility restoration in rapeseed is not published, taking advantages of gene-based markers, make rapeseed breeding program more efficient regarding time and costs.

Updates on Genomic Resources in Chickpea for Crop Improvement

In recent years, rapid advancement has been done in generation of genomic resources for the important legume crop chickpea. Here, we provide an update on important advancements made on availability of genomic resources for this crop. The availability of reference genome and transcriptome sequences, and resequencing of several accessions have enabled the discovery of gene space and molecular markers in chickpea. These resources have helped in elucidating evolutionary relationship and identification of quantitative trait loci for important agronomic traits. Gene expression in different tissues/organs during development and under abiotic/biotic stresses has been interrogated. In addition, single-base resolution DNA methylation patterns in different organs have been analyzed to understand gene regulation. Overall, we provide a consolidated overview of available genomic resources of chickpea that may help in fulfilling the promises for improvement of this important crop.

Legume genomics and transcriptomics: From classic breeding to modern technologies

Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs.

Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.

KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping

MOTIVATION

Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool.

RESULTS

To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results.

AVAILABILITY AND IMPLEMENTATION

Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives

Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.

Adapting legume crops to climate change using genomic approaches

Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.

Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.)

Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76-87% and 90-95% recurrent parent genome recovery, respectively. On the other hand, 90-97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea.

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.

The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 samples at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated.

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.

De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development

Background

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus.

Results

Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions.

Conclusions

This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0531-5) contains supplementary material, which is available to authorized users.

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.

Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea (Cicer arietinum L.)

Flowering time is an important trait for adaptation and productivity of chickpea in the arid and the semi-arid environments. This study was conducted for molecular mapping of genes/quantitative trait loci (QTLs) controlling flowering time in chickpea using F₂ populations derived from four crosses (ICCV 96029 × CDC Frontier, ICC 5810 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier). Genetic studies revealed monogenic control of flowering time in the crosses ICCV 96029 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier, while digenic control with complementary gene action in ICC 5810 × CDC Frontier. The intraspecific genetic maps developed from these crosses consisted 75, 75, 68 and 67 markers spanning 248.8 cM, 331.4 cM, 311.1 cM and 385.1 cM, respectively. A consensus map spanning 363.8 cM with 109 loci was constructed by integrating four genetic maps. Major QTLs corresponding to flowering time genes efl-1 from ICCV 96029, efl-3 from BGD 132 and efl-4 from ICC 16641 were mapped on CaLG04, CaLG08 and CaLG06, respectively. The QTLs and linked markers identified in this study can be used in marker-assisted breeding for developing early maturing chickpea.

Development of molecular map and identification of QTLs linked to Fusarium wilt resistance in chickpea

A number of genetic maps for Fusarium wilt resistance in chickpea have been reported in earlier studies, however QTLs identified for Fusarium wilt resistance were unstable. Hence, the present study aims to map novel molecular markers and to identify QTLs for Fusarium wilt resistance in chickpea. An intraspecific linkage map of chickpea (Cicer arietinum L.) was constructed using F10-F11 recombinant inbred lines (RILs) derived from a cross between K850 and WR315 segregating for H2 locus. A set of 31 polymorphic simple sequence repeat (SSR) markers obtained by screening 300 SSRs and were used for genotyping. The linkage map had four linkage groups and coverage of 690 cM with a marker density of 5.72 cM. The RILs were screened for their wilt reaction across two seasons in wilt sick plot at International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, India. Five major quantitative trait loci (QTLs) were detected in both seasons for late wilting (60 days after sowing). A stable QTL (GSSR 18-TC14801) for wilt resistance was identified in both the seasons, and the QTL explained a variance of 69.80 and 60.80% in 2007 and 2008 rabi respectively.

Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1-45-bp)-based ILP (intron-length polymorphism) markers from 3283 genes were developed that were structurally and functionally annotated on eight chromosomes and unanchored scaffolds of chickpea. A much higher amplification efficiency (83%) and intra-specific polymorphic potential (86%) detected by these markers than that of other sequence-based genetic markers among desi and kabuli chickpea accessions was apparent even by a cost-effective agarose gel-based assay. The genome-wide physically mapped 1718 ILP markers assayed a wider level of functional genetic diversity (19-81%) and well-defined phylogenetics among domesticated chickpea accessions. The gene-derived 1424 ILP markers were anchored on a high-density (inter-marker distance: 0.65cM) desi intra-specific genetic linkage map/functional transcript map (ICC 4958×ICC 2263) of chickpea. This reference genetic map identified six major genomic regions harbouring six robust QTLs mapped on five chromosomes, which explained 11-23% seed weight trait variation (7.6-10.5 LOD) in chickpea. The integration of high-resolution QTL mapping with differential expression profiling detected six including one potential serine carboxypeptidase gene with ILP markers (linked tightly to the major seed weight QTLs) exhibiting seed-specific expression as well as pronounced up-regulation especially in seeds of high (ICC 4958) as compared to low (ICC 2263) seed weight mapping parental accessions. The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database". The designing of multiple ISM and ILP markers (2-5 markers/gene) from an individual gene (transcription factor) with numerous aforementioned desirable genetic attributes can widen the user-preference to select suitable primer combination for simultaneous large-scale assaying of functional allelic variation, natural allelic diversity, molecular mapping and expression profiling of genes among chickpea accessions. This will essentially accelerate the identification of functionally relevant molecular tags regulating vital agronomic traits for genomics-assisted crop improvement by optimal resource expenses in chickpea.