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Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom ® CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

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 BC3F3 in Pusa 372; 20 BC2F3 in Pusa 362, and 21 BC3F3 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.

Domain swapping and generation of chimeric insecticidal crystal protein is an emerging area of insect pest management. The lepidopteran insect pest, gram pod borer ( H.) wreaks havoc to chickpea crop affecting production. Lepidopteran insects were reported to be controlled by ( ) genes. We designed a plant codon optimized chimeric gene ( ) using three domains from three different genes (domains I, II, and III from , , and , respectively) and expressed it under the control of a constitutive promoter in chickpea ( . DCP92-3) to assess its effect on gram pod borer. A total of six transgenic chickpea shoots were established by grafting into mature fertile plants. The regenerated (organogenetic) shoots were selected based on antibiotic kanamycin monosulfate (100 mg/L) with transformation efficiency of 0.076%. Three transgenic events were extensively studied based on gene expression pattern and insect mortality across generations. Protein expression in pod walls, immature seeds and leaves (pre- and post-flowering) were estimated and expression in pre-flowering stage was found higher than that of post-flowering. Analysis for the stable integration, expression and insect mortality (detached leaf and whole plant bioassay) led to identification of efficacious transgenic chickpea lines. The chimeric expressed in chickpea is effective against gram pod borer and generated events can be utilized in transgenic breeding program.

Chickpea ( L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea. This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs), of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13,778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavor of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.

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

Key messageIntegration 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.

The rich genetic diversity existing within exotic, indigenous, and diverse germplasm lays the foundation for the continuous improvement of crop cultivars. The composite collection has been suggested as a gateway to identifying superior germplasm for use in crop improvement programs. Here, a chickpea global composite collection was evaluated at five locations in India over two years for five agronomic traits to identify agronomically superior accessions. The desi, kabuli, and intermediate types of chickpea accessions differed significantly for plant height (PLHT) and 100-seed weight (100 SW). In contrast, the intermediate type differed substantially from kabuli for days to maturity (DM). Several highly significant trait correlations were detected across different locations. The most stable and promising accessions from each of the five locations were prioritised based on their superior performance over the best-performing check cultivar. Accordingly, the selected germplasm accessions of desi type showed up to 176% higher seed yield (SY), 29% lower flowering time, 21% fewer maturity days, 64% increase in PLHT, and 183% larger seeds than the check cultivar JG11 or Annigeri. The prioritised kabuli accessions displayed up to 270% more yield, 13% less flowering time, 8% fewer maturity days, 111% increase in PLHT, and 41% larger seeds over the check cultivar KAK2. While the intermediate type accessions had up to 169% better yield, 1% early flowering, 3% early maturity, 54% taller plants, and 25% bigger seeds over the check cultivar JG 11 or KAK2. These accessions can be utilised in chickpea improvement programs to develop high-yielding, early flowering, short duration, taller, and large-seeded varieties with a broad genetic base.

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.

In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.