Using RNA sequencing to unravel molecular changes underlying the defense response in chickpea induced by Phytophthora medicaginis.

Phytophthora root rot (PRR), caused by Phytophthora medicaginis, is a major soil-borne disease of chickpea in Australia. Breeding for PRR resistance is an effective approach to avoid significant yield loss. Genetic resistance has been identified in cultivated chickpea (Cicer arietinum) and in the wild relative C. echinospermum, with previous studies identifying independent genetic loci associated with each of these sources. However, the molecular mechanisms associated with PRR resistance are not known. RNA sequencing analysis employed in this study identified changes in gene expression in roots of three chickpea genotypes grown hydroponically, early post-infection with P. medicaginis zoospores. Analyses of differentially expressed genes (DEG) identified the activation of a higher number of non-specific R-genes in a PRR-susceptible variety than in the resistant genotypes, suggesting a whole plant resistance response occurring in chickpea against the pathogen. Contrasting molecular changes in signaling profiles, proteolysis and transcription factor pathways were observed in the cultivated and wild Cicer-derived resistant genotypes. DEG patterns supported a hypothesis that increased root elongation and reduced adventitious root formation limit the pathogen entry points in the genotype containing the wild Cicer source of PRR resistance. Candidate resistance genes, including an aquaporin and a maltose transporter in the wild Cicer source and GDSL esterases/lipases in the cultivated source of resistance, were oppositely regulated. Increased knowledge of these genes and pathways will improve our understanding of molecular mechanisms controlling PRR resistance in chickpea, and support the development of elite chickpea varieties through molecular breeding approaches.

2024 Australia-New Zealand Expert Consensus Statement on Cardiac Amyloidosis.

Over the past 5 years, early diagnosis of and new treatments for cardiac amyloidosis (CA) have emerged that hold promise for early intervention. These include non-invasive diagnostic tests and disease modifying therapies. Recently, CA has been one of the first types of cardiomyopathy to be treated with gene editing techniques. Although these therapies are not yet widely available to patients in Australia and New Zealand, this may change in the near future. Given the rapid pace with which this field is evolving, it is important to view these advances within the Australian and New Zealand context. This Consensus Statement aims to update the Australian and New Zealand general physician and cardiologist with regards to the diagnosis, investigations, and management of CA.

The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data.

KEY MESSAGE: QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple diversity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two diversity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1-FTa2-FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and diversity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the diversity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.

A QTL on the Ca7 chromosome of chickpea affects resistance to the root-lesion nematode Pratylenchus thornei.

The root-lesion nematode Pratylenchus thornei Sher & Allen, 1953 is a damaging parasite of many crop plants, including the grain legume chickpea (Cicer arietinum L.). Within cultivated chickpea, there are no known sources of strong resistance to P. thornei, but some cultivars have partial resistance. In the research reported here, the genetic basis for differences in P. thornei resistance was analysed using a population derived by accelerated single seed descent from a cross between a partially resistant cultivar, PBA HatTrick, and a very susceptible cultivar, Kyabra. A genetic linkage map was constructed from genotyping-by-sequencing data. Two quantitative trait loci were mapped, one on the Ca4 chromosome and one on the Ca7 chromosome. The Ca7 locus had a greater and more consistent effect than the Ca4 locus. Marker assays designed for single nucleotide polymorphisms on Ca7 were applied to a panel of chickpea accessions. Some of these markers should be useful for marker-assisted selection in chickpea breeding. Haplotype analysis confirmed the Iranian landrace ICC14903 to be the source of the resistance allele in PBA HatTrick and indicated that other Australian cultivars inherited the same allele from other Iranian landraces. A candidate region was defined on the Ca7 pseudomolecule. Within that region, 69 genes have been predicted with high confidence. Among these, two have annotations related to biotic stress response. Three others have previously been reported to be expressed in roots of PBA HatTrick and Kyabra, including one that is more highly expressed in PBA HatTrick than in Kyabra. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01271-8.

Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars.

Environmental constraints severely restrict crop yields in most production environments, and expanding the use of variation will underpin future progress in breeding. In semi-arid environments boron toxicity constrains productivity, and genetic improvement is the only effective strategy for addressing the problem. Wheat breeders have sought and used available genetic diversity from landraces to maintain yield in these environments; however, the identity of the genes at the major tolerance loci was unknown. Here we describe the identification of near-identical, root-specific boron transporter genes underlying the two major-effect quantitative trait loci for boron tolerance in wheat, Bo1 and Bo4 (ref. 2). We show that tolerance to a high concentration of boron is associated with multiple genomic changes including tetraploid introgression, dispersed gene duplication, and variation in gene structure and transcript level. An allelic series was identified from a panel of bread and durum wheat cultivars and landraces originating from diverse agronomic zones. Our results demonstrate that, during selection, breeders have matched functionally different boron tolerance alleles to specific environments. The characterization of boron tolerance in wheat illustrates the power of the new wheat genomic resources to define key adaptive processes that have underpinned crop improvement.

Impact of the NHS Stop Smoking Services on smoking prevalence in England: a simulation modelling evaluation.

BACKGROUND: The English National Health Service NHS Stop Smoking Services (SSS), established in 2001, were the first such services in the world. An appropriate evaluation of the SSS has national and international significance. This modelling study sought to evaluate the impact of the SSS on changes in smoking prevalence in England. METHODS: A discrete time state-transition model was developed to simulate changes in smoking status among the adult population in England during 2001-2016. Input parameters were based on data from national statistics, population representative surveys and published literature. The main outcome was the percentage point reduction in smoking prevalence attributable to the SSS. RESULTS: Smoking prevalence was reduced by 10.8 % in absolute terms during 2001-2016 in England, and 15.3 % of the reduction could be attributable to the SSS. The percentage point reduction in smoking prevalence each year was on average 0.72%, and 0.11 % could be attributable to the SSS. The proportion of SSS supported quit attempts increased from 5.5 % in 2001, to as high as 18.9 % in 2011, and then reduced to 8.2 % in 2016. Quit attempts with SSS support had a higher success rate than those without SSS support (15.1% vs 11.3%). Smoking prevalence in England continued to decline after the SSS was much reduced from 2013 onwards. CONCLUSIONS: Approximately 15% of the percentage point reduction in smoking prevalence during 2001-2016 in England may be attributable to the NHS SSS, although uncertainty remains regarding the actual impact of the formal smoking cessation services.

Future smoking prevalence by socioeconomic status in England: a computational modelling study.

BACKGROUND: The difference in smoking across socioeconomic groups is a major cause of health inequality. This study projected future smoking prevalence by socioeconomic status, and revealed what is needed to achieve the tobacco-free ambition (TFA) by 2030 in England. METHODS: Using data from multiple sources, the adult (≥18 years) population in England was separated into subgroups by smoking and highest educational qualification (HEQ). A discrete time state-transition model was used to project future smoking prevalence by HEQ deterministically and stochastically. RESULTS: In a status quo scenario, smoking prevalence in England is projected to be 10.8% (95% uncertainty interval: 9.1% to 12.9%) by 2022, 7.8% (5.5% to 11.0%) by 2030 and 6.0% (3.7% to 9.6%) by 2040. The absolute difference in smoking rate between low and high HEQ is reduced from 12.2% in 2016 to 7.9% by 2030, but the relative inequality (low/high HEQ ratio) is increased from 2.48 in 2016 to 3.06 by 2030. When applying 2016 initiation/relapse rates, achievement of the TFA target requires no changes to future cessation rates among adults with high qualifications, but increased rates of 37% and 149%, respectively, in adults with intermediate and low qualifications. CONCLUSIONS: If the current trends continue, smoking prevalence in England is projected to decline in the future, but with substantial differences across socioeconomic groups. Absolute inequalities in smoking are likely to decline and relative inequalities in smoking are likely to increase in future. The achievement of England's TFA will require the reduction of both absolute and relative inequalities in smoking by socioeconomic status.

A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform.

Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na(+) ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na(+)-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na(+) ion binding site. Our data enhance the understanding of the permeation functions of Bot1.

Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.

KEY MESSAGE: Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.

Impact of the NHS stop smoking services on smoking prevalence in England: a simulation modelling evaluation.

BACKGROUND: The English National Health Service (NHS) Stop Smoking Services (SSS), established in 2001, were the first such services in the world. An appropriate evaluation of the SSS has national and international significance. This modelling study sought to evaluate the impact of the SSS on changes in smoking prevalence in England. METHODS: A discrete time state-transition model was developed to simulate changes in smoking status among the adult population in England during 2001-2016. Input parameters were based on data from national statistics, population representative surveys and published literature. The main outcome was the percentage point reduction in smoking prevalence attributable to the SSS. RESULTS: Smoking prevalence was reduced by 10.8% in absolute terms during 2001-2016 in England, and 15.1% of the reduction could be attributable to the SSS. The percentage point reduction in smoking prevalence each year was on average 0.72%, and 0.11% could be attributable to the SSS. The proportion of SSS supported quit attempts increased from 5.6% in 2001, to as high as 19.3% in 2011, and then reduced to 8.4% in 2016. Quit attempts with SSS support had a higher success rate than those without SSS support (15.1%vs11.7%). Smoking prevalence in England continued to decline after the SSS was much reduced from 2013 onwards. CONCLUSIONS: Approximately 15% of the percentage point reduction in smoking prevalence during 2001-2016 in England may be attributable to the NHS SSS, although uncertainty remains regarding the actual impact of the formal smoking cessation services.

Factors associated with access to care and healthcare utilization in the homeless population of England.

Background: People experiencing homelessness are known to have complex health needs, which are often compounded by poor access to healthcare. This study investigates the individual-level factors associated with access to care and healthcare utilization among homeless people in England. Methods: A cross-sectional sample of 2505 homeless people from 19 areas of England was used to investigate associations with access to care and healthcare utilization. Results: Rough sleepers were much less likely to be registered with a general practitioner (GP) (odds ratio (OR) 0.45, 95% confidence interval (CI) 0.30-0.66) than single homeless in accommodation (reference group) or the hidden homeless (OR 1.48, 95% CI 0.88-2.50). Those who had recently been refused registration by a GP or dentist also had lower odds of being admitted to hospital (OR 0.67, 95% CI 0.49-0.91) or using an ambulance (OR 0.73, 95% CI 0.54-0.99). Conclusions: The most vulnerable homeless people face the greatest barriers to utilizing healthcare. Rough sleepers have particularly low rates of GP registration and this appears to have a knock-on effect on admission to hospital. Improving primary care access for the homeless population could ensure that some of the most vulnerable people in society are able to access vital hospital services which they are currently missing out on.

QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea.

Terminal drought is a major constraint to chickpea productivity. Two component traits responsible for reduction in yield under drought stress include reduction in seeds size and root length/root density. QTL-seq approach, therefore, was used to identify candidate genomic regions for 100-seed weight (100SDW) and total dry root weight to total plant dry weight ratio (RTR) under rainfed conditions. Genomewide SNP profiling of extreme phenotypic bulks from the ICC 4958 × ICC 1882 population identified two significant genomic regions, one on CaLG01 (1.08 Mb) and another on CaLG04 (2.7 Mb) linkage groups for 100SDW. Similarly, one significant genomic region on CaLG04 (1.10 Mb) was identified for RTR. Comprehensive analysis revealed four and five putative candidate genes associated with 100SDW and RTR, respectively. Subsequently, two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR were validated using CAPS/dCAPS markers. Identified candidate genomic regions and genes may be useful for molecular breeding for chickpea improvement.

Phenotypic plasticity and its genetic regulation for yield, nitrogen fixation and δ13C in chickpea crops under varying water regimes.

We measured yield components, nitrogen fixation, soil nitrogen uptake and carbon isotope composition (δ(13)C) in a collection of chickpea genotypes grown in environments where water availability was the main source of yield variation. We aimed to quantify the phenotypic plasticity of these traits using variance ratios, and to explore their genetic basis using FST genome scan. Fifty-five genes in three genomic regions were found to be under selection for plasticity of yield; 54 genes in four genomic regions for the plasticity of seeds per m(2); 48 genes in four genomic regions for the plasticity of δ(13)C; 54 genes in two genomic regions for plasticity of flowering time; 48 genes in five genomic regions for plasticity of nitrogen fixation and 49 genes in three genomic regions for plasticity of nitrogen uptake from soil. Plasticity of yield was related to plasticity of nitrogen uptake from soil, and unrelated to plasticity of nitrogen fixation, highlighting the need for closer attention to nitrogen uptake in legumes. Whereas the theoretical link between δ(13)C and transpiration efficiency is strong, the actual link with yield is erratic due to trade-offs and scaling issues. Genes associated with plasticity of δ(13)C were identified that may help to untangle the δ(13)C-yield relationship. Combining a plasticity perspective to deal with complex G×E interactions with FST genome scan may help understand and improve both crop adaptation to stress and yield potential.

Clinical Characteristics and Outcomes of Patients with Amphetamine-Associated Cardiomyopathy in South Auckland, New Zealand.

BACKGROUND: Amphetamine-associated cardiomyopathy (AAC) is becoming an increasingly recognised entity. The characteristics and outcomes of these patients are poorly understood. METHODS: Thirty patients admitted with heart failure and echocardiographic evidence of cardiomyopathy between 2005 and 2014 and who had a documented history of amphetamine abuse that was considered an important factor in the causation of their cardiomyopathy were retrospectively identified. RESULTS: Mean age at presentation was 40±10 years with a male predominance (n=25, 83%). The majority were of indigenous Maori ethnicity. At presentation, four patients were in cardiogenic shock. Five patients required intensive care unit (ICU) admission for inotropic support and mechanical ventilation. Fifteen had severe left ventricular (LV) dilation (mean LV end-diastolic dimension 6.8±1.0cm) and all patients had severe LV dysfunction (mean LV ejection fraction 22±8%). Despite optimal heart failure therapy, LV size remained significantly dilated with minimal improvement in LV function. During median follow-up of 18 months, five patients died from end-stage heart failure and 17 had at least one readmission with decompensated heart failure. CONCLUSION: Amphetamine-associated cardiomyopathy was seen predominantly in young indigenous Maori men. They presented with severe cardiomyopathy, often requiring ICU admission. Severe LV dilation and significant LV dysfunction persisted despite treatment and mortality was high.

Diversity in boron toxicity tolerance of Australian barley (Hordeum vulgare L.) genotypes.

BACKGROUND: Boron (B) is an important micronutrient for plant growth, but is toxic when levels are too high. This commonly occurs in environments with alkaline soils and relatively low rainfall, including many of the cereal growing regions of southern Australia. Four major genetic loci controlling tolerance to high soil B have been identified in the landrace barley, Sahara 3771. Genes underlying two of the loci encode the B transporters HvBot1 and HvNIP2;1. RESULTS: We investigated sequence and expression level diversity in HvBot1 and HvNIP2;1 across barley germplasm, and identified five novel coding sequence alleles for HvBot1. Lines were identified containing either single or multiple copies of the Sahara HvBot1 allele. We established that only the tandemly duplicated Sahara allele conferred B tolerance, and this duplicated allele was found only in a set of nine lines accessioned in Australian collections as Sahara 3763-3771. HvNIP2;1 coding sequences were highly conserved across barley germplasm. We identified the likely causative SNP in the 5'UTR of Sahara HvNIP2;1, and propose that the creation of a small upstream open reading frame interferes with HvNIP2;1 translation in Sahara 3771. Similar to HvBot1, the tolerant HvNIP2;1 allele was unique to the Sahara barley accessions. We identified a new source of the 2H B tolerance allele controlling leaf symptom development, in the landrace Ethiopia 756. CONCLUSIONS: Ethiopia 756, as well as the cultivar Sloop Vic which carries both the 2H and HvBot1 B tolerance alleles derived from Sahara 3771, may be valuable as alternative parents in breeding programs targeted to high soil B environments. There is significant diversity in B toxicity tolerance among contemporary Australian barley varieties but this is not related to variation at any of the four known B tolerance loci, indicating that novel, as yet undiscovered, sources of tolerance exist.

Genotyping-by-sequencing based intra-specific genetic map refines a ''QTL-hotspot" region for drought tolerance in chickpea.

To enhance the marker density in the "QTL-hotspot" region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the "QTL-hotspot" region. These efforts have refined the "QTL-hotspot" region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the "QTL-hotspot" region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus.

KEY MESSAGE: We characterise the distribution of crossover and non-crossover recombination in Brassica napus and Cicer arietinum using a low-coverage genotyping by sequencing pipeline SkimGBS. The growth of next-generation DNA sequencing technologies has led to a rapid increase in sequence-based genotyping for applications including diversity assessment, genome structure validation and gene-trait association. We have established a skim-based genotyping by sequencing method for crop plants and applied this approach to genotype-segregating populations of Brassica napus and Cicer arietinum. Comparison of progeny genotypes with those of the parental individuals allowed the identification of crossover and non-crossover (gene conversion) events. Our results identify the positions of recombination events with high resolution, permitting the mapping and frequency assessment of recombination in segregating populations.

A Nurse Practitioner Clinic: A Novel Approach to Supporting Patients Following Heart Valve Surgery.

BACKGROUND: Valvular heart disease is an important healthcare issue and its impacts are increasing. Following valve surgery, traditional models of care involve medical personnel, however, significant gaps in guideline adherence and delays in follow-up have been reported. Internationally, there is increasing evidence that specialist nurses can function in a variety of clinical settings and improve patient management. METHODS: In 2009, a nurse practitioner clinic to support patients following valve surgery was established. We used a retrospective clinical audit and clinical review with descriptive statistics to describe the development of the clinic and to provide guidance for other services for model of care development. RESULTS: Over four years, 462 patients have been reviewed at least once, with over half having multiple assessments, 37% had rheumatic heart disease. These patients were 20 years younger and more likely to be women, non-European, current smokers and have atrial fibrillation. All patients received a focussed lifestyle, rheumatic, thromboembolic and endocarditis risk and symptom review with tailored support, advice and referral where appropriate. Four percent were referred back to a cardiologist for early evidence of valve dysfunction and a further 1.5% required urgent admission for unstable symptoms. CONCLUSION: The nurse practitioner clinic offers a systematic approach to promoting guideline adherence post valvular surgery. Important clinical symptoms and differences in health needs were identified and were actioned appropriately.

Comparative transcriptome analysis reveals molecular regulation of salt tolerance in two contrasting chickpea genotypes.

Salinity is a major abiotic stress that causes substantial agricultural losses worldwide. Chickpea (Cicer arietinum L.) is an important legume crop but is salt-sensitive. Previous physiological and genetic studies revealed the contrasting response of two desi chickpea varieties, salt-sensitive Rupali and salt-tolerant Genesis836, to salt stress. To understand the complex molecular regulation of salt tolerance mechanisms in these two chickpea genotypes, we examined the leaf transcriptome repertoire of Rupali and Genesis836 in control and salt-stressed conditions. Using linear models, we identified categories of differentially expressed genes (DEGs) describing the genotypic differences: salt-responsive DEGs in Rupali (1,604) and Genesis836 (1,751) with 907 and 1,054 DEGs unique to Rupali and Genesis836, respectively, salt responsive DEGs (3,376), genotype-dependent DEGs (4,170), and genotype-dependent salt-responsive DEGs (122). Functional DEG annotation revealed that the salt treatment affected genes involved in ion transport, osmotic adjustment, photosynthesis, energy generation, stress and hormone signalling, and regulatory pathways. Our results showed that while Genesis836 and Rupali have similar primary salt response mechanisms (common salt-responsive DEGs), their contrasting salt response is attributed to the differential expression of genes primarily involved in ion transport and photosynthesis. Interestingly, variant calling between the two genotypes identified SNPs/InDels in 768 Genesis836 and 701 Rupali salt-responsive DEGs with 1,741 variants identified in Genesis836 and 1,449 variants identified in Rupali. In addition, the presence of premature stop codons was detected in 35 genes in Rupali. This study provides valuable insights into the molecular regulation underpinning the physiological basis of salt tolerance in two chickpea genotypes and offers potential candidate genes for the improvement of salt tolerance in chickpeas.

Fine Mapping of a Vigor QTL in Chickpea (Cicer arietinum L.) Reveals a Potential Role for Ca4_TIFY4B in Regulating Leaf and Seed Size.

Plant vigor is a complex trait for which the underlying molecular control mechanisms remain unclear. Vigorous plants tend to derive from larger seeds and have greater early canopy cover, often with bigger leaves. In this study, we delimited the size of a major vigor quantitative trait locus (QTL) on chickpea chromosome 4-104.4 kb, using recombinant association analysis in 15 different heterogeneous inbred families, derived from a Rupali/Genesis836 recombinant inbred line population. The phenotypic and molecular genetic analysis provided evidence for a role of the gene Ca4_TIFY4B, in determining leaf and seed size in chickpea. A non-synonymous single-nucleotide polymorphism (SNP) in the high-vigor parent was located inside the core motif TIFYCG, resulting in a residue change T[I/S]FYCG. Complexes formed by orthologs of Ca4_TIFY4B (PEAPOD in Arabidopsis), Novel Interactor of JAZ (CaNINJA), and other protein partners are reported to act as repressors regulating the transcription of downstream genes that control plant organ size. When tested in a yeast 2-hybrid (Y2H) assay, this residue change suppressed the interaction between Ca4_TIFY4B and CaNINJA. This is the first report of a naturally occurring variant of the TIFY family in plants. A robust gene-derived molecular marker is available for selection in chickpea for seed and plant organ size, i.e., key component traits of vigor.