Integrating genomics for chickpea improvement: achievements and opportunities

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

How rising temperatures would be detrimental for cool and warm-season food legumes

Rising temperatures are a major concern for the productivity of food legumes, grown in winter as well as summer-season, especially in tropical and sub-tropical regions. Our studies have indicated marked damage to the reproductive stage, resulting in reduction in pod set and seed yield of chickpea, lentil (cool-season legumes) and mungbean (warm-season legume) under high temperatures. Studies done in controlled and outdoor environments (late sowing) revealed that temperatures >35/20°C (as day and night) were highly detrimental for winter-season legumes; while >38/25°C markedly affected the summer-season legumes (mungbean). Urdbean, (a summer season legume), was found to be relatively more tolerant. The degree of damage varies depending upon the duration, timing and severity of stress. Among the reproductive components, pollen grains were more sensitive, became deformed and showed reduction in pollen viability, reduced germination and pollen tube growth. Stigma receptivity and ovule viability were also inhibited, which affected the pollen germination on stigma surface and restricted tube growth through style, and impaired fertilization to cause flower abortion. Assessment of the physiology of leaves, anthers and styles indicated decrease in sucrose production in all these organs due to inhibition of enzymes, which possibly affected the structural and functional aspects of the pollen grains and tube growth through style. Seed filling is another stage which becomes impaired as a result of inactivation of enzymes related to sucrose production, causing inhibition in sucrose translocation into seeds. Additionally, the composition of the seeds was adversely affected, resulting in small size and poor quality of seeds. The data related to these processes would be presented. Genetic variation for heat tolerance exists in our target legume crops, which needs further probing and use of heat tolerant germplasm in breeding programs. Screening for high temperature tolerance has led to identification of few heat-tolerant genotypes, which are able to maintain their gamete function at high temperature, unlike the sensitive genotypes. Future studies should focus on high throughput phenotyping techniques and/or physiological, biochemical or genetic markers that control the reproductive function. Information about the effects of heat stress on reproductive biology and seed filling events of chickpea, lentil and mungbean will be discussed

Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops

Key message We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. Abstract In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of diverse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their individual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops

Salinity tolerance and ion accumulation in chickpea (Cicer arietinum L.) subjected to salt stress

Chickpea (Cicer arietinum L.) is considered a salt sensitive species, but some genetic variation for salinity tolerance exists. The present study was initiated to determine the degree of salt tolerance among chickpea genotypes, and the relationship between salt tolerance and ion accumulation in leaves and reproductive tissues. Methods Three experiments were conducted in a glasshouse in Perth, Western Australia, in which up to 55 genotypes of chickpea were subjected to 0, 40 or 60 mM NaCl added to the soil to determine the variation in salt tolerance, and the association between salt tolerance and reproductive success. Pod and seed numbers, seed yield and yield components, pollen viability, in vitro pollen germination and in vivo pollen tube growth, were used to evaluate reproductive success. Leaves, flowers and seeds were sampled in the reproductive phase to measure the concentrations of sodium, potassium and chloride ions in these organs. Results When grown in soil with 40 mM NaCl, a 27-fold range in seed yield was observed among the 55 chickpea genotypes. The increased salt tolerance, as measured by yield under salinity or relative yield under saline conditions, was positively associated with higher pod and seed numbers, and higher shoot biomass, but not with time to 50 % flowering nor with the number of filled pods in the non-saline treatment. Pod abortion was higher in the salt sensitive genotypes, but pollen viability, in vitro pollen germination and in vivo pollen tube growth were not affected by salinity in either the salt tolerant or salt sensitive genotypes. The concentrations of sodium and potassium ions, but not chloride, in the seed were significantly higher in the sensitive (106 μmol g−1 DM of sodium and 364 μmol g−1 DM of potassium) than in the tolerant (74 and 303 μmol g−1 DM, respectively) genotypes. Sodium and potassium, but particularly chloride, ions accumulated in leaves and in pod wall, whereas accumulation in the seed was much lower. Conclusions Considerable genotypic variation for salt tolerance exists in chickpea germplasm. Selection for genotypes with high pod and/or seed numbers that accumulate low concentrations of salt in the seed will be beneficial

Abrasion resistance and compressive strength of unprocessed rice husk ash concrete

This paper investigates the effects of adding natural rice husk ash collected from uncontrolled burning and without previous grinding (NRHA) as cement replacement in concrete. To obtain an adequate particle size, NRHA was mixed with coarse aggregate for a convenient period of time before adding the other components. Compressive strength, water absorption, porosity, and abrasion resistance expressed as weight loss were examined. Test results show that decreasing the particle size through mixing with coarse aggregate improved the compressive strength, reduced the permeability, and increased the abrasion resistance of concrete. By mixing NRHA with aggregate for 8 min, abrasion resistance improved by 10.35 and 23.62% over the control concrete at 28 and 91 days, respectively. Incorporating NRHA in concrete by grinding with coarse aggregate during the mixing process could be suitable for making normal-strength concrete and for applications where abrasion resistance is an important parameter. In addition, using NRHA as a partial replacement cement contributes to the reduction of CO2 emissions due to the production of cement

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

Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches

Background - The major proteins in lupin seeds are conglutins that have primary roles in supplying carbon, sulphur and nitrogen and energy for the germinating seedling. They fall into four families; α, β, γ and δ. Interest in these conglutins is growing as family members have been shown to have beneficial nutritional and pharmaceutical properties. Results - An in-depth transcriptome and draft genome from the narrow-leafed lupin (NLL; Lupinus angustifolius) variety, Tanjil, were examined and 16 conglutin genes were identified. Using RNAseq data sets, the structure and expression of these 16 conglutin genes were analysed across eight lupin varieties from five lupin species. Phylogenic analysis suggest that the α and γ conglutins diverged prior to lupin speciation while β and δ members diverged both prior and after speciation. A comparison of the expression of the 16 conglutin genes was performed, and in general the conglutin genes showed similar levels of RNA expression among varieties within species, but quite distinct expression patterns between lupin species. Antibodies were generated against the specific conglutin families and immunoblot analyses were used to compare the levels of conglutin proteins in various tissues and during different stages of seed development in NLL, Tanjil, confirming the expression in the seed. This analysis showed that the conglutins were expressed highly at the mature seed stage, in all lupin species, and a range of polypeptide sizes were observed for each conglutin family. Conclusions - This study has provided substantial information on the complexity of the four conglutin families in a range of lupin species in terms of their gene structure, phylogenetic relationships as well as their relative RNA and protein abundance during seed development. The results demonstrate that the majority of the heterogeneity of conglutin polypeptides is likely to arise from post-translational modification from a limited number of precursor polypeptides rather than a large number of different genes. Overall, the results demonstrate a high degree of plasticity for conglutin expression during seed development in different lupin species

Negative regulation of signal transducer and activator of transcription-3 signalling cascade by lupeol inhibits growth and induces apoptosis in hepatocellular carcinoma cells

Background: Constitutive activation of signal transducer and activator of transcription signalling 3 (STAT3) has been linked with survival, proliferation and angiogenesis in a wide variety of malignancies including hepatocellular carcinoma (HCC). Methods: We evaluated the effect of lupeol on STAT3 signalling cascade and its regulated functional responses in HCC cells. Results: Lupeol suppressed constitutive activation of STAT3 phosphorylation at tyrosine 705 residue effectively in a dose- and time-dependent manner. The phosphorylation of Janus-activated kinases (JAKs) 1 and 2 and Src was also suppressed by lupeol. Pervanadate treatment reversed the downregulation of phospho-STAT3 induced by lupeol, thereby indicating the involvement of a phosphatase. Indeed, we observed that treatment with lupeol increased the protein and mRNA levels of SHP-2, and silencing of SHP-2 abolished the inhibitory effects of lupeol on STAT3 activation. Treatment with lupeol also downregulated the expression of diverse STAT3-regulated genes and decreased the binding of STAT3 to VEGF promoter. Moreover, the proliferation of various HCC cells was significantly suppressed by lupeol, being associated with substantial induction of apoptosis. Depletion of SHP-2 reversed the observed antiproliferative and pro-apoptotic effects of lupeol. Conclusions: Lupeol exhibited its potential anticancer effects in HCC through the downregulation of STAT3-induced pro-survival signalling cascade