Figure 3 - uploaded by Sivakumar Chamarthi
Content may be subject to copyright.
Phenotypic evaluation of three root traits in selected introgression lines (ILs). Analysis of phenotyping data for root traits namely root depth (a), root length density (b), and root dry weight (c) of selected ILs show better root traits as compared to the recurrent parent and in some cases to even the donor parent. cyl, cylinder.
Source publication
A "QTL-hotspot" containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker-assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0...
Similar publications
The effect of gamma rays and ethylmethane sulphonate (EMS) mutagens on seed germination and plant survival of four chickpea (Cicer arietinum L.) genotypes including two desi (Pb2000 and C44), one kabuli (Pb-1) and one desi x kabuli introgression genotype (CH40/91) was investigated in the M1 generation under field conditions. Seed germination and pl...
A chickpea (Cicer arietinum L.) cultivar, GPF2, was crossed with two accessions, EC556270 and ILWC21, of its wild relative C. reticulatum with the objective to introgress productivity enhancing traits from wild to cultivated chickpea. The F 1s were backcrossed to cultivated parent to generate backcross derived generations and also selfed to generat...
There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without...
Citations
... The genomic regions containing multiple QTLs for different traits, also called QTL hotspots, enable simultaneous selection and accelerating the breeding progress through MAS [90]. The present study reported four co-localized QTLs, viz., qSS.7A. 1 (Table 7). ...
Background
Drought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% of Brassica juncea (Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87 B. carinata-derived B. juncea introgression lines (ILs) was developed with the goal of creating drought-tolerant genotypes.
Method
The experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map.
Results
The linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed by B. carinata (BC 4), suggesting a greater contribution of B. carinata towards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome of B. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz., SOS2, SOS2 like, NPR1, FAE1-KCS, HOT5, DNAJA1, NIA1, BRI1, RF21, ycf2, WRKY33, PAL, SAMS2, orf147, MAPK3, WRR1 and SUS, were reported in the genomic regions of identified QTLs.
Conclusions
The significance of B. carinata in improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
... Therefore, serious efforts are required for the accurate characterization of the existing germplasm against these traits, as well as drought and heat stress tolerance utilizing high-throughput screening techniques. Molecular mapping-based QTL identification and transcriptome analysis have paved the way to dissect the complexity of traits imparting drought and heat tolerance (Table S1) [91,[248][249][250][251][252][253][254]. This led to the identification of major QTLs or candidate genes for heat and drought tolerance in chickpeas [154]. ...
Although chickpea (Cicer arietinum L.) has high yield potential, its seed yield is often low and unstable due to the impact of abiotic stresses, such as drought and heat. As a result of global warming, both drought and heat are estimated to be major yield constraints between one-quarter and one-third per annum. In the present review, genomic-mediated breeding strategies to increase resilience against global warming. Exacerbated drought and heat stresses have been examined to understand the latest advancement happening for better management of these challenges. Resistance mechanisms for drought and heat stresses consist of (i) escape via earliness, (ii) avoidance via morphological traits such as better root traits, compound leaves, or multipinnate leaves and double-/multiple-podded traits, and (iii) tolerance via molecular and physiological traits, such as special tissue and cellular abilities. Both stresses in chickpeas are quantitatively governed by minor genes and are profoundly influenced by edaphic and other environmental conditions. High-yield genotypes have traditionally been screened for resistance to drought and heat stresses in the target selection environment under stress conditions or in the simulacrum mediums under controlled conditions. There are many drought- and heat-tolerant genotypes among domestic and wild Cicer chickpeas, especially in accessions of C. reticulatum Ladiz., C. echinospermum P.H. Davis, and C. turcicum Toker, J. Berger, and Gokturk. The delineation of quantitative trait loci (QTLs) and genes allied to drought- and heat-related attributes have paved the way for designing stress-tolerant cultivars in chickpeas. Transgenic and “omics” technologies hold newer avenues for the basic understanding of background metabolic exchanges of QTLs/candidate genes for their further utilization. The overview of the effect of drought and heat stresses, its mechanisms/adaptive strategies, and markers linked to stress-related traits with their genetics and sources are pre-requisites for framing breeding programs of chickpeas with the intent of imparting drought tolerance. Ideotype chickpeas for resistance to drought and heat stresses were, therefore, developed directly using marker-aided selection over multiple locations. The current understanding of molecular breeding supported by functional genomics and omics technologies in developing drought- and heat-tolerant chickpea is discussed in this review.
... Many studies among several crop species have employed plant genetic resources (PGR) to detect quantitative trait loci (QTL) that can harbor beneficial alleles at loci for relevant phenotypic traits under challenging environments [7][8][9][10]. In chickpea, valuable QTLs from landraces against abiotic and biotic stress factors and improved root growths have been introgressed by marker-assisted backcrossing into cultivars [11,12]. Other methods for the introgression under salinity and control conditions, among others [48,49]. ...
Precise and high-throughput phenotyping (HTP) of vegetative drought tolerance in chickpea plant genetic resources (PGR) would enable improved screening for genotypes with low relative loss of biomass formation and reliable physiological performance. It could also provide a basis to further decipher the quantitative trait drought tolerance and recovery and gain a better understanding of the underlying mechanisms. In the context of climate change and novel nutritional trends, legumes and chickpea in particular are becoming increasingly important because of their high protein content and adaptation to low-input conditions. The PGR of legumes represent a valuable source of genetic diversity that can be used for breeding. However, the limited use of germplasm is partly due to a lack of available characterization data. The development of HTP systems offers a perspective for the analysis of dynamic plant traits such as abiotic stress tolerance and can support the identification of suitable genetic resources with a potential breeding value. Sixty chickpea accessions were evaluated on an HTP system under contrasting water regimes to precisely evaluate growth, physiological traits, and recovery under optimal conditions in comparison to drought stress at the vegetative stage. In addition to traits such as Estimated Biovolume (EB), Plant Height (PH), and several color-related traits over more than forty days, photosynthesis was examined by chlorophyll fluorescence measurements on relevant days prior to, during, and after drought stress. With high data quality, a wide phenotypic diversity for adaptation, tolerance, and recovery to drought was recorded in the chickpea PGR panel. In addition to a loss of EB between 72% and 82% after 21 days of drought, photosynthetic capacity decreased by 16–28%. Color-related traits can be used as indicators of different drought stress stages, as they show the progression of stress.
... The filtered high-quality reads were mapped on the kabuli chickpea genome (v1.0; Varshney et al., 2013b) using Tophat (v2.1.1) (Trapnell et al., 2009) software. ...
... QTL-hotspot region plays a major role in drought tolerance in chickpea, and its introgression in an elite variety (JG 11) improved the root traits and drought tolerance (Varshney et al., 2013b). Integration of QTL information and co-expression network analysis has been exploited successfully for the identification of potential candidate genes associated with the maize kernel starch content (Lin et al., 2019a). ...
Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.
... In this study, graphical genotypes facilitated confirming parental lineages among population/individuals and introgression studies for desirable genes etc. There were no reports of exclusively constructing graphical genotypes using SNP data for confirming introgressions in chickpea; however, graphical genotypes were made for confirming introgression of drought tolerance using SSRs (Varshney et al. 2013). The present investigation, thus, proved that C. pinnatifidum, an underutilized wild species, housing adequate variability for morphological traits, productivity traits like pods per plant and seeds per pods along with the good levels of resistance against AB and BGM diseases. ...
... ICC 4958 exhibited the least DRR-wilt disease incidence and highest yields under both well-watered and drought conditions compared to the other genotypes. ICC 4958 is a drought-resistant genotype, with greater root length density and root depth compared to JG 62 and JG 11 (Kashiwagi et al., 2006;Varshney et al., 2013). The genotype is also resistant to wilt and DRR (Chilakala et al., 2022;Sharma et al., 2010). ...
Context or problem
Root rots, a major factor contributing to yield loss in chickpea, often occur in disease complexes.
Objective or research question
Plant responses to disease complexes are not well elucidated. We sought a clear understanding of a newly identified disease complex in chickpea, dry root rot (DRR)–wilt disease complex, in the field and studied the effect of drought on the severity of the complex and its effect on yield. We compared plant responses to DRR alone and the disease complex under drought and determined the phytohormones involved in plant defense against the disease complex.
Methods
We compared the effect of 14 environments (two soil moisture regimes at seven locations) on the incidence of the disease complex and yield loss in four chickpea genotypes. We also studied the effect of drought on rhizospheric and root endo-microbial communities by whole-genome and metagenomic sequencing and performed LC-MS-based phytohormonal profiling of chickpea roots.
Results
Soil moisture and plant genetic variability were critical in modulating disease incidence in field conditions. DRR was the primary driver of the disease complex under drought stress. Drought aggravated the yield reductions caused by the disease complex from 35% to 60% in susceptible genotypes. Further, drought-tolerant genotypes performed better under combined disease complex infection and drought stress and exhibited lesser yield losses than susceptible genotypes. Pathogenic fungi such as Macrophomina phaseolina, Fusarium oxysporum, and Rhizoctonia solani were enriched in the chickpea rhizosphere, and M. phaseolina was predominant in infected chickpea roots under both well-watered and drought conditions. Symbiotic associations of chickpea with nitrogen-fixing bacteria were suppressed under drought stress. Abscisic acid, jasmonic acid, and salicylic acid were found to be involved in defense against the disease complex across various stages of plant growth.
Implications or significance
We highlight the interaction between drought and soil pathogens affecting chickpea yield and suggest the utilization of drought-tolerant root traits as donor traits for improving combined stress resistance. We also demonstrate growth stage–dependent phytohormonal responses elicited by DRR and the DRR–wilt disease complex. The identification and management of root rots is essential, and our findings offer valuable new insights into a lesser-known but highly significant disease complex of chickpea.
... Therefore, assembly validation is a must for any draft genome. The first draft genome of chickpea was released in 2013 on the kabuli type chickpea variety CDC Frontier (Varshney et al. 2013b). Subsequently, a desi variety ICC 4958 genome draft was reported (Jain et al. 2013 . ...
... Similar to MARS, advanced backcross QTL (AB-QTL) is another molecular breeding scheme that does not need predefined gene-trait associations (Tanksley and Nelson 1996). Given its ability to capture the tremendous genetic variation present in AB-QTL scheme tried in chickpea at ICRISAT , Varshney et al. 2013b). Mapping of important traits will facilitate identification of tightly linked markers for marker-assisted selection. ...
Worldwide, abiotic stresses including heat and drought are the major obstructions that threaten the agricultural production. Development of climate-resilient cultivars is the easy and economical way to combat drought and heat stress with limited resources. Plants do follow adaptation strategies to mitigate the impact of stress and lead to alteration in some of the morphological traits such as leaf rolling, leaf angle, cuticular wax content, stomatal conductance, deep root system, altered signalling and metabolic pathways. Targeting such traits along with the economical yield will help to identify suitable genotypes which perform better under stress environment. The basic step is to explore the available physiological trait variation among the cultivars, germplasm set and wild relatives to main stream alleles of importance to breeding material from the donor parent. Conventional and advanced breeding strategies can be implemented to develop climate-resilient cultivars with the suitable breeding and screening methods. As a key factor hybridization and selection along with the implication of advanced breeding methods like MABB, MARS, GS and transgenic approach make it easy and accurate to develop varieties in less time. Linkage, QTL and genome-wide association mapping helps to identify the genomic region of interest to target during marker-aided breeding approaches. A cocktail of breeding methods from conventional to transgenic may help in the development of high-yielding climate-resilient varieties which can help to serve farmers to escape from glitch of crop loss due to dry spell during cropping season. The recent advancement and methodologies regarding drought and heat tolerance breeding in wheat are discussed in this chapter along with the difficulties posed.KeywordsDroughtHeatWheatPhysiological breedingMolecular markers
... icrisat.org/). The MABC technique has been used in the development of introgression of QTLs into elite cultivars in order to develop introgressed lines (Bharadwaj and Yadav, 2012;Varshney et al., 2013b;Barmukh et al., 2022). The 'Pusa Chickpea 20211' variety is another example in which resistance genes for multiple races (foc 1,2,3,4, and 5) of fusarium wilt have been stacked through MABC in the mega desi chickpea variety 'Pusa 391' (Bharadwaj et al., 2022). ...
... The identification of a QTL-hotspot region in linkage group 4 (CaLG04) in chickpea that harbors major QTLs for multiple drought adaptive traits, followed by its introgression into elite chickpea cultivars, is an excellent example of genomics-assisted breeding (Barmukh et al., 2022). This region accounts for 58.2% of explained phenotypic variation and a 16% yield enhancement under drought conditions in introgressed lines, which is primarily attributed to improvements in root traits, such root length, density, surface area, and volume (Varshney et al., 2013b;Roorkiwal et al., 2020;Bharadwaj et al., 2021). ...
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
... However, for the sustainable utilization of genetic resources, advanced techniques, such as NGS, HPG, and HTP, should be used to develop new crop varieties to ensure food security in the near future. MABC Resistance to nematode [123,124] MABC Enhanced oleic acid [125,126] Chickpea MABC Resistance to fusarium wilt [127] MABC Resistance to Ascochyta blight [127] MABC Drought tolerance [128] MABC Elimination of lipoxygenase-2, [121] MAS-marker-assisted selection; MABB-marker-assisted backcross breeding; MABC-marker-assisted backcross. ...
Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the demand for genetic resources will increase as the world population increases. There is a need to conserve and maintain the genetic diversity of these valuable resources for sustainable food security. Due to environmental changes and genetic erosion, some valuable genetic resources have already become extinct. The landraces, wild relatives, wild species, genetic stock, advanced breeding material, and modern varieties are some of the important plant genetic resources. These diverse resources have contributed to maintaining sustainable biodiversity. New crop varieties with desirable traits have been developed using these resources. Novel genes/alleles linked to the trait of interest are transferred into the commercially cultivated varieties using biotechnological tools. Diversity should be maintained as a genetic resource for the sustainable development of new crop varieties. Additionally, advances in biotechnological tools, such as next-generation sequencing, molecular markers, in vitro culture technology, cryopreservation, and gene banks, help in the precise characterization and conservation of rare and endangered species. Genomic tools help in the identification of quantitative trait loci (QTLs) and novel genes in plants that can be transferred through marker-assisted selection and marker-assisted backcrossing breeding approaches. This article focuses on the recent development in maintaining the diversity of genetic resources, their conservation, and their sustainable utilization to secure global food security.
... Chickpea (Cicer arietinum L.), a rich source of protein, carbohydrates, and minerals and therefore provides a major supply of nutrients in vegetarian diets particularly in developing countries . In chickpea, several studies have been carried out for fine mapping the "QTLhotspot" region to identify the candidate genes linked with DS tolerance and development of closely associated markers (Varshney et al., 2013(Varshney et al., , 2014Jaganathan et al., 2015;Kale et al., 2015;Bharadwaj et al., 2021). For instance, by employing phenotyping data for 20 DS tolerance-linked traits collected in one to seven seasons at one to five locations in India and genotyping data for 241 simple sequence repeat loci on one intraspecific population (ICC 4958 × ICC 1882), the authors recognized a "QTL-hotspot" region harboring 12 QTLs for 12 DS tolerance-linked traits explaining F I G U R E 3 Proposed scheme for developing drought-smart future crop plants. ...
... Notably, fast-forward breeding can maintain genetic diversity in breeding programs to increase genetic gains from breeding revolutions up to 58.20% percentage variance explained (Varshney et al., 2014). In another study, the introgression of this "QTLhotspot" region in 'JG 11' (an elite cultivar) has improved root traits and DS tolerance (Varshney et al., 2013). In a recent study, these authors reveal that the introgression of the "QTLhotspot" region into three elite chickpea cultivars from India ('Pusa 372', 'Pusa 362', and 'DCP 92-3') improves DS tolerance and seed yield under DS conditions (Bharadwaj et al., 2021). ...
Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS‐associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought‐smart future crops. In short, we recommend incorporating several approaches, such as multi‐omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought‐smart cultivars to achieve the ‘zero hunger’ goal.
