Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.

Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.

Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.

Because of the rise in global temperature, heat stress has become a major concern for crop production. Heat stress deteriorates plant productivity and alters phenological and physiological responses that aid in precise monitoring and sensing of mildto-severe transient heat stress. Plants have evolved several sophisticated mechanisms including hormone-signaling pathways to sense heat stimuli and acquire heat stress tolerance. In response to heat stress, ethylene, a gaseous hormone, is produced which is indispensable for plant growth and development and tolerance to various abiotic stresses including heat stress. The manipulation of ethylene in developing heat stress tolerance targeting ethylene biosynthesis and signaling pathways has brought promising out comes. Conversely increased ethylene biosynthesis and signaling seem to exhibit inhibitory effects in plant growth responses from primitive to maturity stages. This review mainly focuses on the recent studies of ethylene involvement in plant responses to heat stress and its functional regulation, and molecular mechanism underlying the plant responses in the mitigation of heat-induced damages. Furthermore, this review also describes the crosstalk between ethylene and other signaling molecules under heat stress and approaches to improve heat stress tolerance in plants.

The Arabis alpina APETALA2 ortholog, PERPETUAL FLOWERING2, coordinates the age-dependent response to vernalization and it is required to facilitate the activation of A. alpina FLOWERING LOCUS C after vernalization.

Summary The critical role of cytokinin in early nodulation in legumes is well known. In our study, exogenous cytokinin application to roots of the important crop legume, chickpea (Cicer arietinum L.), led to the formation of pseudo‐nodules even in the absence of rhizobia. Hence, a genome‐wide analysis of the cytokinin signalling, two‐component system (TCS) genes, was conducted in chickpea, Medicago and Cajanus cajan. The integrated phylogenetic, evolutionary and expression analysis of the TCS genes was carried out, which revealed that histidine kinases (HKs) were highly conserved, whereas there was diversification leading to neofunctionalization at the level of response regulators (RRs) especially the TypeB RRs. Further, the functional role of the CaHKs in nodulation was established by complementation of the sln1Δ mutant of yeast and cre1 mutants of (Medicago) which led to restoration of the nodule‐deficient phenotype. Additionally, the highest expressing TypeB RR of chickpea, CaRR13, was functionally characterized. Its localization in the nucleus and its Y1H assay‐based interaction with the promoter of the early nodulation gene CaNSP2 indicated its role as a transcription factor regulating early nodulation. Overexpression, RNAi lines and complementation of cre1 mutants with CaRR13 revealed its critical involvement as an important signalling molecule regulating early events of nodule organogenesis in chickpea.

TITLE 1 PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in 2 Arabis alpina 3 4 5 RUNNING TITLE 6 PEP2 coordinates flowering in response to vernalization 7 8 HIGHLIGHT 9The Arabis alpina APETALA2 orthologue, PERPETUAL FLOWERING2, regulates the age-10 dependent response to vernalization and it is required to facilitate the activation of the A. 11 alpina FLOWERING LOCUS C after vernalization. 12 13 ABSTRACT 14 The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age 15 pathway. The AP2 orthologue in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 16 2 (PEP2), was previously reported to regulate flowering through the vernalization pathway by 17 enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the 18 orthologue of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering 19 independently of PEP1. To characterize the function of PEP2 we analyzed the transcriptomes 20 of pep2 and pep1 mutants. The majority of differentially expressed genes were detected 21 between pep2 and the wild type or between pep2 and pep1, highlighting the importance of 22 the PEP2 role that is independent of PEP1. Here we demonstrate that PEP2 prevents the 23 upregulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY) 24 and APETALA1 (AaAP1) which ensure floral commitment during vernalization. Young pep2 25 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent 26 response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-27 dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in 28 4 the main shoot apex and in the axillary branches. These multiple roles of PEP2 in vernalization 29 response contribute to the A. alpina life-cycle. 30 31 KEY WORDS: APETALA2, AP2, juvenility, FLOWERING LOCUS C, FLC, perennial, PERPETUAL 32 FLOWERING 1, PEP1, PEP2, vernalization 33 34 ABBREVIATIONS: 35 DAG: Days after germination 36 LDs: Long days 37 SDs: Short days 38 39box transcription factor FLOWERING LOCUS C (FLC) is the major regulator of flowering in 56 response to vernalization (Michaels and Amasino, 1999; Sheldon et al., 2000). FLC 57 transcriptionally regulates floral integrator genes such as SUPPRESSOR OF OVEREXPRESSION 58 OF CONSTANS1 (SOC1), and genes involved in the age pathway, suggesting an interplay 59 between these two pathways (Deng et al., 2011; Mateos et al., 2017). Comparative studies 60 between Arabidopsis and the alpine perennial Arabis alpina demonstrated that the FLC 61 orthologue in A. alpina, PERPETUAL FLOWERING1 (PEP1), also regulates flowering in response 62 to vernalization. In addition, PEP1 contributes to the perennial growth habit by repressing 63 flowering in a subset of axillary meristems after vernalization (Lazaro et al., 2018; Wang et al., 64 2009). Flower buds in A. alpina are formed during prolonged exposure to vernalizing 65 conditions. The length of vernalization deter...

Linker H1 histones play an important role in animal and human pathogenesis, but their function in plant immunity is poorly understood. Here, we analyzed mutants of the three canonical variants of Arabidopsis H1 histones, namely H1.1, H1.2 and H1.3. We observed that double h1.1h1.2 and triple h1.1h1.2h1.3 (3h1) mutants were resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis of 3h1 mutant plants showed that histone H1s play a key role in regulating the expression of early and late defense genes upon pathogen challenge. Moreover, 3h1 mutant plants showed enhanced production of reactive oxygen species and activation of mitogen activated protein kinases upon pathogen-associated molecular pattern (PAMP) treatment. However, 3h1 mutant plants were insensitive to priming with flg22, a well-known bacterial PAMP which induces enhanced resistance in WT plants. The defective defense response in 3h1 was correlated with the enhanced DNA methylation and reduced H3K56ac levels upon priming. Our data place H1 as a molecular gatekeeper in governing dynamic changes in the chromatin landscape of defense genes during plant pathogen interaction.