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Non-chimeric regeneration via in vitro mutagenesis is one of the niche areas in perennial fruit crops to shorten the breeding cycle. However, the recovery of M1 population is a major hurdle due to lack of efficient protocols. Hence the present experiment was conducted during 2021–23 at ICAR-Indian Agricultural Research Institute, New Delhi on EMS induced in vitro mutagenesis and its validation in kinnow mandarin (Citrus nobilis Loureiro × Citrus deliciosa Tenora). The specialized direct somatic embryogenesis (DSE) protocol was standardized and the optimized explants (in ovulo nucellus) were treated with 3 EMS concentration of 0.1, 0.5 and 1.0% for 1, 3 and 5 h. Based on explant survival, probit analysis was calculated and results revealed that the LD50 for in ovulo nucellus explants was 0.3% for 5 h. For a dose rate higher than LD50 i.e. E8 (0.5% for 5 h) and as compared to control, the embryogenesis efficiency was reduced to 65%, likewise embryo production (23.64%), germination (46.15%), conversion (22.76%), establishment (25.85%) and acclimatization (19.44%) showed reducing trend. The EMS derived M1 population showed variability both at morphological and molecular level. Among the markers tested, random amplification of polymorphic DNA (RAPD) and simple sequence repeats (SSR) could demarcate the mutants from mother plant. The origin of homohistont was confirmed from the morphology of observed chlorophyll defective mutants. Thus the optimized EMS dose using DSE system can be effectively used for production of trait specific solid mutants and the morphological and molecular screening protocols have practical value in early selection of M1 population.

Most chickpea cultivation occurs in rainfed environments, where unpredictable rainfall leads to drought stress, consequently reducing growth and productivity. Fast and robust image-based screening methods would greatly facilitate drought tolerance research. In this study, an experiment was conducted in a climate-controlled environment, using radio frequency-enabled ID (RFID) tagged plant carriers on Lemnatec's high-throughput phenotyping platform. The agro-physiological characteristics of six chickpea genotypes under drought stress conditions imposed at the early podding stage were explored. Using non-destructive techniques, including Red, Green, and, Blue (RGB), Near-Infrared (NIR), Infrared (IR), and chlorophyll fluorescence (Fv/Fm) imaging, data was captured at various stages of drought stress, quantified as the fraction of transpirable soil water, using LemnaGrid software. Traits such as plant phenology, yield, yield components, and physiological parameters (e.g., leaf temperature and photosynthetic characteristics) for both drought-stressed and well-watered plants were recorded manually. Seed yields ranged from 9.9 to 18.1 g plant−1 under WW, and 2.6–13.7 g plant−1 under DS. DS decreased yield the most in ICC 1882 and RSG 888 (73.7%) and the least in ICC 4958 (24.3%) relative to WW. Our findings revealed significant genotype × water treatment interactions for all manually recorded traits. Moreover, strong positive correlations were observed between manually recorded and image-based traits, i.e., between aboveground dry weight and projected area, aboveground dry weight and convex hull area, plant height and caliper length, photosynthetic rate, and chlorophyll fluorescence, stomatal conductance and NIR reflectance, IR thermometer temperature and IR imaging temperature. Notably, the strong positive correlations between NIR reflectance and stomatal conductance, and between chlorophyll fluorescence and photosynthesis, underscore the immense potential of harnessing image-based screening methods in breeding programs to enhance drought tolerance.

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.

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.

In chickpea breeding, drought is a major concern and a complex trait controlled by several genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over the years, the landraces have proven to be a good source for the dissection of genes for different yield and yield-related traits. The present investigation for marker-trait associations (MTAs) and candidate gene identification was conducted by studying 125 chickpea landraces collected from the West Asia and North Africa (WANA) region, along with 4 varieties suitable for irrigated and rainfed environments. This study analyzed 13 physio-morphological traits in 2 consecutive years at two isolated locations (IARI, New Delhi, and Dharwad). A strong correlation coefficient was observed between the trait seed yield (SY) and biological yield (BY) under both conditions. The Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at the IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6,367 single nucleotide polymorphisms (SNPs) distributed across the genome were used for genetic diversity study, population structure, and genome-wide association study (GWAS). The average polymorphic information content (PIC) value observed was 0.25, and the average linkage disequilibrium (LD) decay distance was 152,269 bp across the genome. A total of four subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for the GWAS analysis, which considered both fixed- and random-effect models. A total of 52 significant SNPs were reported in both irrigated and rainfed conditions at low locations; 7 SNPs were associated with more than one trait, which may have pleiotropic effects. Significant SNPs were annotated in the pulse database. The identified genomic region found in or near MTA under rainfed conditions encodes for guard cell hydrogen peroxideresistant1 (GHR1), late embryogenesis-abundant, E3 ubiquitin-protein ligase, walls are thin1 (WAT1), and beta-galactosidase that are known to be associated with drought tolerance. [ABSTRACT FROM AUTHOR]

Summary: Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground‐breaking work, especially his effort to list orphan tropical crops to genomic resource‐rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape. [ABSTRACT FROM AUTHOR]

Identifying a congenially targeted production environment and understanding the effects of genotype by environmental interactions on the adaption of chickpea genotypes is essential for achieving an optimal yield stability. Different models like additive main effect and multiplicative interactions (AMMI 1, AMM2), weighted average absolute scores of BLUPs (WAASB), and genotype plus genotype–environment (GGE) interactions were used to understand their suitability in the precise estimation of variance and their interaction. Our experiment used genotypes that represent the West Asia–North Africa (WANA) region. This trial involved two different sowing dates, two distinct seasons, and three different locations, resulting in a total of 12 environments. Genotype IG 5871(G1) showed a lower heat susceptibility index (HSI) across environments under study. The first four interactions principal component axis (IPCA) explain 93.2% of variations with significant genotype–environment interactions. Considering the AMMI stability value (ASV), the genotypes IG5862(G7), IG5861(G6), ILC239(G40), IG6002(G26), and ILC1932(G39), showing ASV scores of 1.66, 1.80, 2.20, 2.60, and 2.84, respectively, were ranked as the most stable and are comparable to the weighted average absolute scores of BLUPs (WAASB) ranking of genotypes. The which–won–where pattern of genotype plus genotype–environment (GGE) interactions suggested that the target environment consists of one mega environment. IG5866(G10), IG5865(G9), IG5884(G14), and IG5862(G7) displayed higher stability, as they were nearer to the origin. The genotypes that exhibited a superior performance in the tested environments can serve as ideal parental lines for heat-stress tolerance breeding programs. The weighted average absolute scores of BLUPs (WAASB) serve as an ideal tool to discern the variations and identify the stable genotype among all methods. [ABSTRACT FROM AUTHOR]

Context: Chickpea (Cicer arietinum L.) are highly sensitive to elevated salinity, particularly at initial seedling establishment stage. Seedling screening would be an effective means to identify novel sources of donors for salt tolerance. Aim: This study aimed to identify salt stress tolerant genotypes at seedling stage from 50 chickpea accessions. Methods: The screening of 50 chickpea accessions was done under two salinity conditions including salt stress (8 dS m−1) and control (no salt stress). Accessions were studied for morphological traits, root system architectural analysis, and CSTI (Cumulative salt tolerance index). Further, principal component analysis was conducted to validate these results for more accuracy and reliability. Key results: For morphological traits, a high degree of genetic variation was seen among genotypes, and root traits were found to be the better indicators of salt stress tolerance. CSTI was used to classify the accessions; 22 (44%) were identified as salt sensitive, 21 (42%) were found to be moderately salt tolerant, and 7 (14%) had moderate to high salt tolerance. The most salt tolerant and salt sensitive genotypes were found to be ICCV10 and ILC5595, respectively. Conclusions: Early seedling screening has a great potential to identify genotypes with robust root systems, which can withstand salinity. Implications: We used a novel approach to classify chickpea landraces based on the combination of CSTI and principal component analysis methods. By choosing suitable donors and prospective genotypes at early growth stages, the knowledge gathered from this study may aid scientists and chickpea breeders in developing salt tolerant cultivars. Salinity is a major problem in chickpea; landraces were used to identify novel sources using a seedling screening technique. We find two analysis methods (cumulative salt tolerance index and principal components analysis) that enable salt tolerant genotypes to be identified; and both techniques were equally reliable.. We identified ICCV10, CSG8962, ILC11902, IG5980, IG5893 as five salt tolerant genotypes. [ABSTRACT FROM AUTHOR]

Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped extensively for yield and yield related traits at two different locations (Delhi and Patancheru, India) during the crop seasons 2011-12 and 2012-13 under rainfed and irrigated conditions. In parallel, these lines were also genotyped using DArTseq platform to generate data on 3,000 polymorphic markers. Phenotypic and genotypic data were used with six statistical GS models to estimate the prediction accuracies. GS models were tested for four yield related traits viz. seed yield, 100 seed weight, days to 50% flowering and days to maturity. Prediction accuracy for the models tested varied from 0.138 (seed yield) to 0.912 (100 seed weight), whereas performance of models did not show any significant difference for estimating prediction accuracy within traits. Kinship matrix calculated using genotyping data reaffirmed existence of two different groups within selected lines. There was not much effect of population structure on prediction accuracy. In brief, present study establishes the necessary resources for deployment of GS in chickpea breeding.