A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Fast-forward breeding for a food-secure world.

Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.

Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society.

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.

Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention.

BACKGROUND: Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others. RESULTS: Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences. CONCLUSION: The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain's adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.

Developing future heat-resilient vegetable crops.

Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.

Copper removal capability and genomic insight into the lifestyle of copper mine inhabiting Micrococcus yunnanensis GKSM13.

Heavy metal pollution in mining areas is a serious environmental concern. The exploration of mine-inhabiting microbes, especially bacteria may use as an effective alternative for the remediation of mining hazards. A highly copper-tolerant strain GKSM13 was isolated from the soil of the Singhbhum copper mining area and characterized for significant copper (Cu) removal potential and tolerance to other heavy metals. The punctate, yellow-colored, coccoid strain GKSM13 was able to tolerate 500 mg L-1 Cu2+. Whole-genome sequencing identified strain GKSM13 as Micrococcus yunnanensis, which has a 2.44 Mb genome with 2176 protein-coding genes. The presence of putative Cu homeostasis genes and other heavy metal transporters/response regulators or transcription factors may responsible for multi-metal resistance. The maximum Cu2+ removal of 89.2% was achieved at a pH of 7.5, a temperature of 35.5 °C, and an initial Cu2+ ion concentration of 31.5 mg L-1. Alteration of the cell surface, deposition of Cu2+ in the bacterial cell, and the involvement of hydroxyl, carboxyl amide, and amine groups in Cu2+ removal were observed using microscopic and spectroscopic analysis. This study is the first to reveal a molecular-based approach for the multi-metal tolerance and copper homeostasis mechanism of M. yunnanensis GKSM13.

Comprehensive Transcriptome Profiling Uncovers Molecular Mechanisms and Potential Candidate Genes Associated with Heat Stress Response in Chickpea.

Chickpea (Cicer arietinum L.) production is highly susceptible to heat stress (day/night temperatures above 32/20 °C). Identifying the molecular mechanisms and potential candidate genes underlying heat stress response is important for increasing chickpea productivity. Here, we used an RNA-seq approach to investigate the transcriptome dynamics of 48 samples which include the leaf and root tissues of six contrasting heat stress responsive chickpea genotypes at the vegetative and reproductive stages of plant development. A total of 14,544 unique, differentially expressed genes (DEGs) were identified across different combinations studied. These DEGs were mainly involved in metabolic processes, cell wall remodeling, calcium signaling, and photosynthesis. Pathway analysis revealed the enrichment of metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction, under heat stress conditions. Furthermore, heat-responsive genes encoding bHLH, ERF, WRKY, and MYB transcription factors were differentially regulated in response to heat stress, and candidate genes underlying the quantitative trait loci (QTLs) for heat tolerance component traits, which showed differential gene expression across tolerant and sensitive genotypes, were identified. Our study provides an important resource for dissecting the role of candidate genes associated with heat stress response and also paves the way for developing climate-resilient chickpea varieties for the future.

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.

Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea.

'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.

QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea.

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut.

Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.

Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut.

Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut.

Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations.

The present study reports profiling of the elevated carbon dioxide (CO2) concentration responsive global transcriptome in chickpea, along with a combinatorial approach for exploring interlinks between physiological and transcriptional changes, important for the climate change scenario. Various physiological parameters were recorded in two chickpea cultivars (JG 11 and KAK 2) grown in open top chambers under ambient [380 parts per million (ppm)] and two stressed/elevated CO2 concentrations (550 and 700 ppm), at different stages of plant growth. The elevated CO2 concentrations altered shoot and root length, nodulation (number of nodules), total chlorophyll content and nitrogen balance index, significantly. RNA-Seq from 12 tissues representing vegetative and reproductive growth stages of both cultivars under ambient and elevated CO2 concentrations identified 18,644 differentially expressed genes including 9,687 transcription factors (TF). The differential regulations in genes, gene networks and quantitative real-time polymerase chain reaction (qRT-PCR) -derived expression dynamics of stress-responsive TFs were observed in both cultivars studied. A total of 138 pathways, mainly involved in sugar/starch metabolism, chlorophyll and secondary metabolites biosynthesis, deciphered the crosstalk operating behind the responses of chickpea to elevated CO2 concentration.

Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.).

Haplotype-based breeding, a recent promising breeding approach to develop tailor-made crop varieties, deals with identification of superior haplotypes and their deployment in breeding programmes. In this context, whole genome re-sequencing data of 292 genotypes from pigeonpea reference set were mined to identify the superior haplotypes for 10 drought-responsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene-based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker-trait associations (MTAs) in five genes influencing seven drought-responsive component traits. Haplo-pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. The haplotype C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight (TW), the haplotype C. cajan_30211-H6 for PW, FW, TW and dry weight (DW), the haplotype C. cajan_26230-H11 for FW and DW and the haplotype C. cajan_26230-H5 for relative water content (RWC) were identified as superior haplotypes under drought stress condition. Furthermore, 17 accessions containing superior haplotypes for three drought-responsive genes were identified. The identified superior haplotypes and the accessions carrying these superior haplotypes will be very useful for deploying haplotype-based breeding to develop next-generation tailor-made better drought-responsive pigeonpea cultivars.

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications.

Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.

Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea.

Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.

Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post-transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.