Comparative time series RNA-seq analysis of Pigeonpea Root Tissues in response to Fusarium udum infection

Pigeonpea [Cajanus cajan (L.) Millsp.] is an important food legume and is mostly cultivated in tropical and subtropical regions of South Asia, Kenya, Malawi, Bangladesh, and other parts of the world. India is the center of origin and major global producer (66%), consumer, and importer, ahead of production in Africa (14%)..

Global gene expression analysis of pigeonpea with male sterility conditioned by A 2 cytoplasm

Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility-inducing cytoplasm have been reported, of which A2 and A4 have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene (nad7) and A4-CMS has been demonstrated in pigeonpea; however, the mechanism underlying A2-CMS still remains obscure. The current investigation aimed to analyze the differences in A2-CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next-generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A2-CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea

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 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

Evaluation of global composite collection reveals agronomically superior germplasm accessions for chickpea improvement

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

Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes

In Extended Data Fig. 1 of this Article, the labels ‘Market class’ and ‘Biological status’ were inadvertently swapped. In the corresponding figure legend, “Track 1: Biological status; Track 2: Market class;” should have been “Track 1: Market class; Track 2: Biological status;”. The original Article has been corrected online

Physio-morphological and molecular analysis for salt tolerance in chickpea (Cicer arietinum)

After drought salinity is the major abiotic stress that severely affects agricultural productivity globally. Chickpea(Cicer arietinum L.) is the important grain legume which suffers approximately 8-10% of total global yield loss due to salinity. Screening for salt stress is difficult and traits that correlate salinity tolerance are least understood. The present study was carried out at ICAR-IARI, New Delhi 2017-18, deals with the important morphological and physiological traits like RWC (Relative water content), EL (Electrolyte Leakage), Na/K (sodium and potassium ratio) to characterize the salt tolerant genotypes under hydroponic condition which is a quick and easy method to screen large number of chickpea genotypes at initial stage under salt stress condition. Genotypes showing high RWC, low EL and Na/K ratio were tolerant like ICCV 10, JG 11, JG 62 and CSG-8962 whereas genotypes like ICC4958 and Pusa362 fall under moderately tolerant genotypes and DCP 93-3, Pusa 256, Phule G5 and SBD 377 were classified as susceptible genotypes. This study also attempts to understand the candidate genes responsible for salt-stress related pathways in chickpea genotypes based on sequence similarity approach exploiting known salt-stress responsive genes from model crops or other crop species

Utility of informative SSR Markers in the molecular characterization of cytoplasmic genetic male Sterility-Based hybrid and its parents in pigeonpea

Pigeonpea is one of the most important pulse crops in the semi-arid tropical region, which is prone to several climatic uncertainties like unpredictable temperature, frequent drought and inconsistent rainfall. Additionally, during crop cycle pigeonpea also encounters a wide range of other biotic and abiotic constraints, ultimately leading to its fluctuating production and stagnant productivity. However, recently developed CGMS system has shown noteworthy impacts in enhancing pigeonpea productivity through exploitation of hybrid vigour. At present, A2-cytoplasm derived CGMS system has been well established in pigeonpea. Nevertheless, the commercial success of CGMS system relies largely on the continuous supply of genetically pure seeds of hybrids and corresponding parental lines. Traditionally, the genetic purity of seeds is guaranteed through conducting grow out test (GoT). In this context, DNA marker assays offer several advantages over conventional GoT especially in terms of time, space and money. Given its locus-specific and co-dominant nature, SSR or microsatellite marker is particularly suited for hybridity testing and purity assessment. Here we report a set of robust SSR markers, which could act as reliable molecular kit for ensuring the genetic purity of the CGMS-hybrid ‘IPH 09-5’ and its parental lines ‘PA 163A’ (A-or Male sterile-line) and ‘AK 261322’ (R- or Restorer-line)

Breeding for abiotic stress tolerance in pulses using genomic tools

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Discovery of putative herbicide resistance genes and its regulatory network in chickpea using transcriptome sequencing

Background: Chickpea (Cicer arietinum 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. Results: 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. Conclusion: 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