Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.).
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ABSTRACT:
SUBMITTER: Barmukh R
PROVIDER: S-EPMC8121343 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Chickpea, the second most important legume crop, suffers major yield losses by terminal drought stress (DS). Stronger root system is known to enhance drought yields but this understanding remains controversial. To understand precisely the root traits contribution towards yield, 12 chickpea genotypes with well-known drought response were field evaluated under drought and optimal irrigation. Root traits, such as root length density (RLD), total root dry weight (RDW), deep root dry weight (deep RDW) and root:shoot ratio (RSR), were measured periodically by soil coring up to 1.2 m soil depth across drought treatments. Large variations were observed for RLD, RDW, deep RDW and RSR in both the drought treatments. DS increased RLD below 30 cm soil depth, deep RDW, RSR but decreased the root diameter. DS increased the genetic variation in RDW more at the penultimate soil depths. Genetic variation under drought was the widest for RLD ?50 DAS, for deep RDW ?50-75 DAS and for RSR at 35 DAS. Genotypes ICC 4958, ICC 8261, Annigeri, ICC 14799, ICC 283 and ICC 867 at vegetative stage and genotypes ICC 14778, ICCV 10, ICC 3325, ICC 14799 and ICC 1882 at the reproductive phase produced greater RLD. Path- and correlation coefficients revealed strong positive contributions of RLD after 45 DAS, deep RDW at vicinity of maturity and RSR at early podfill stages to yield under drought. Breeding for the best combination of profuse RLD at surface soil depths, and RDW at deeper soil layers, was proposed to be the best selection strategy, for an efficient water use and an enhanced terminal drought tolerance in chickpea.
| S-EPMC5221670 | biostudies-literature
Project description:BackgroundChickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea.ResultsWe present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL.ConclusionThe physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.
| S-EPMC2996997 | biostudies-literature
Project description:Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
| S-EPMC4273598 | biostudies-literature
Project description:The ever-increasing industrial activities over the decades have generated high toxic metal such as chromium (Cr) that hampers the crop productivity. This study evaluated the effect of Cr on two chickpea (Cicer arietinum L.) varieties, Pusa 2085 and Pusa Green 112, in hydroponic and pot-grown conditions. First, growth parameters (seed germination, seedling growth, and biomass production) and physio-biochemical parameters (oxidative stress and the content of antioxidants and proline) were measured to evaluate the performance of both varieties grown hydroponically for 21 days at concentrations of 0, 30, 60, 90 and 120 μM Cr in the form of potassium dichromate (K2Cr2O7). In both varieties, significantly deleterious effects on germination and seedling growth parameters were observed at 90 and 120 μM, while growth was stimulated at 30 μM Cr. Significant increases in malondialdehyde and hydrogen peroxide content and electrolyte leakage demonstrated enhanced oxidative injury to seedlings caused by higher concentrations of Cr. Further, increasing concentrations of Cr positively correlated with increased proline content, superoxide dismutase activity, and peroxide content in leaves. There was also an increase in peroxisomal ascorbate peroxidase and catalase in the leaves of both varieties at lower Cr concentrations, whereas a steep decline was recorded at higher Cr concentrations. In the pot experiments conducted over two consecutive years, growth, yield, yield attributes, grain protein, and Cr uptake and accumulation were measured at different Cr concentrations. Pusa Green 112 showed a significant reduction in plant growth, chlorophyll content, grain protein, pod number, and grain yield per plant when compared with Pusa 2085. Overall, our results indicate that Pusa 2085 has a higher Cr tolerance than Pusa Green 112. Therefore, Pusa 2085 could be used to further elucidate the mechanisms of Cr tolerance in plants and in breeding programmes to produce Cr-resistant varieties.
| S-EPMC7714171 | biostudies-literature
Project description:Under global climate change, high-temperature stress is becoming a major threat to crop yields, adversely affecting plant growth, and ultimately resulting in significant yield losses in various crops, including chickpea. Thus, identifying crop genotypes with increased heat stress (HS) tolerance is becoming a priority for chickpea research. Here, we assessed the response of seven physiological traits and four yield and yield-related traits in 39 chickpea genotypes grown in normal-sown and late-sown environments [to expose plants to HS (>32/20°C) at the reproductive stage] for two consecutive years (2017–2018 and 2018–2019). Significant genetic variability for the tested traits occurred under normal and HS conditions in both years. Based on the tested physiological parameters and yield-related traits, GNG2171, GNG1969, GNG1488, PantG186, CSJ515, RSG888, RSG945, RVG202, and GNG469 were identified as promising genotypes under HS. Further, ten heat-tolerant and ten heat-sensitive lines from the set of 39 genotypes were validated for their heat tolerance (32/20°C from flowering to maturity) in a controlled environment of a growth chamber. Of the ten heat-tolerant genotypes, GNG1969, GNG1488, PantG186, RSG888, CSJ315, and GNG1499 exhibited high heat tolerance evidenced by small reductions in pollen viability, pollen germination, and pod set %, high seed yield plant–1 and less damage to membranes, photosynthetic ability, leaf water status, and oxidative processes. In growth chamber, chlorophyll, photosynthetic efficiency, pollen germination, and pollen viability correlated strongly with yield traits. Thus, GNG1969, GNG1488, PantG186, RSG888, CSJ315, and GNG1499 genotypes could be used as candidate donors for transferring heat tolerance traits to high-yielding heat-sensitive varieties to develop heat-resilient chickpea cultivars.
| S-EPMC9202580 | biostudies-literature
Project description:A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics.
| S-EPMC3082040 | biostudies-literature
Project description:This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.
| S-EPMC4668357 | biostudies-literature
Project description:Key messageA high-density linkage map of chickpea using 3430 SNPs was constructed and used to identify QTLs and candidate genes for ascochyta blight resistance in chickpea. Chickpea cultivation in temperate conditions is highly vulnerable to ascochyta blight infection. Cultivation of resistant cultivars in combination with fungicide application within an informed disease management package is the most effective method to control ascochyta blight in chickpeas. Identifying new sources of resistance is critical for continued improvement in ascochyta blight resistance in chickpea. The objective of this study was to identify genetic loci and candidate genes controlling the resistance to ascochyta blight in recombinant inbred lines derived from crossing cultivars Amit and ICCV 96029. The RILs were genotyped using the genotyping-by-sequencing procedure and Illumina® GoldenGate array. The RILs were evaluated in the field over three site-years and in three independent greenhouse experiments. A genetic map with eight linkage groups was constructed using 3430 SNPs. Eight QTLs for resistance were identified on chromosomes 2, 3, 4, 5 and 6. The QTLs individually explained 7-40% of the phenotypic variations. The QTLs on chromosomes 2 and 6 were associated with the resistance at vegetative stage only. The QTLs on chromosomes 2 and 4 that were previously reported to be conserved across diverse genetic backgrounds and against different isolates of Ascochyta rabiei were confirmed in this study. Candidate genes were identified within the QTL regions. Their co-localization with the underlying QTLs was confirmed by genetic mapping. The candidate gene-based SNP markers would lead to more efficient marker-assisted selection for ascochyta blight resistance and would provide a framework for fine mapping and subsequent cloning of the genes associated with the resistance.
| S-EPMC6531409 | biostudies-literature
Project description:The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to predict microRNAs and phased small interfering RNAs from chickpea. Identification of microRNAs and phased small inferfering RNAs in chickpea (Cicer arietinum) by analyzing small RNA sequencing profiles of leaves and flowers using Illumina GAII.
2015-05-08 | E-GEOD-62216 | biostudies-arrayexpress
Project description:A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot_a" (15 genes) and "QTL-hotspot_b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.
| S-EPMC4609953 | biostudies-literature