Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

Ahmed, Shaimaa M.; Alsamman, Alsamman M.; Jighly, Abdulqader; Mubarak, Mohamed; Al-Shamaa, Khaled; Istanbuli, Tawffiq; Momtaz, Osama A.; Allali, Achraf El; Hamwieh, Aladdin

doi:10.1371/journal.pone.0260709

Cited by 23 publications

(18 citation statements)

References 42 publications

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“…Chickpea is the most important cool-season food legume and provides nutritional food to the growing population [ 1 , 2 ]. With climate change, chickpea will become an increasingly important crop [ 3 , 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

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Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

Kaashyap

Ford

Mann

et al. 2022

Plants

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Salinity is increasingly becoming a significant problem for the most important yet intrinsically salt-sensitive grain legume chickpea. Chickpea is extremely sensitive to salinity during the reproductive phase. Therefore, it is essential to understand the molecular mechanisms by comparing the transcriptomic dynamics between the two contrasting genotypes in response to salt stress. Chickpea exhibits considerable genetic variation amongst improved cultivars, which show better yields in saline conditions but still need to be enhanced for sustainable crop production. Based on previous extensive multi-location physiological screening, two identified genotypes, JG11 (salt-tolerant) and ICCV2 (salt-sensitive), were subjected to salt stress to evaluate their phenological and transcriptional responses. RNA-Sequencing is a revolutionary tool that allows for comprehensive transcriptome profiling to identify genes and alleles associated with stress tolerance and sensitivity. After the first flowering, the whole flower from stress-tolerant and sensitive genotypes was collected. A total of ~300 million RNA-Seq reads were sequenced, resulting in 2022 differentially expressed genes (DEGs) in response to salt stress. Genes involved in flowering time such as FLOWERING LOCUS T (FT) and pollen development such as ABORTED MICROSPORES (AMS), rho-GTPase, and pollen-receptor kinase were significantly differentially regulated, suggesting their role in salt tolerance. In addition to this, we identify a suite of essential genes such as MYB proteins, MADS-box, and chloride ion channel genes, which are crucial regulators of transcriptional responses to salinity tolerance. The gene set enrichment analysis and functional annotation of these genes in flower development suggest that they can be potential candidates for chickpea crop improvement for salt tolerance.

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Section: Introductionmentioning

confidence: 99%

“…Chickpea is intrinsically sensitive to salinity during the reproductive stages, affecting the crop yields [ 1 , 11 ]. It can withstand salinity up to an electrical conductivity (EC) value of less than or equal to 1.0 dS/m compared to cereals, which can tolerate up to an EC equal to 10.0 dS/m [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

Kaashyap

Ford

Mann

et al. 2022

Plants

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“…Integrating genome-wide sequence information with precise phenotypic variation has the potential to detect accessions with Huang and Han, 2014). Owing to its high resolution, cost effectiveness and non-essential pedigrees, association mapping has been able to dissect many important traits in chickpea, such as concentration of mineral nutrients (Diapari et al, 2014;Upadhyaya et al, 2016;Fayaz et al, 2022;Samineni et al, 2022); seed yield (Basu et al, 2018); drought tolerance (Li et al, 2018); root morphology, phosphorous acquisition, and use efficiency (Thudi et al, 2021); and salinity tolerance (Ahmed et al, 2021). The major challenge for GWAS is to control the false positives, primarily caused by population structure and family relatedness (Kaler et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association mapping of nutritional traits for designing superior chickpea varieties

et al. 2022

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Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56–24.64/100 g), β-Carotene (0.003–0.104 mg/100 g), calcium (60.69–176.55 mg/100 g), and folate (0.413–6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation–reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.

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“…The association with the salinity tolerance in the field (Arish, Sinai, Egypt) and the greenhouse by using hydroponic system at 100 mM NaCl concentration indicated one locus on chromosome Ca4 at 10,618,070 bp associated with salinity tolerance, in addition to another locus-specific to the hydroponic system on chromosome Ca2 at 30,537,619 bp. The gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0) (Ahmed et al, 2021). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil.…”

Section: Genome-wide Association Studies For Broadening the Genetic B...mentioning

confidence: 99%

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Singh

Ambika

et al. 2022

Front. Genet.

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Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.

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Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

Cited by 23 publications

References 42 publications

Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

Genome-wide association mapping of nutritional traits for designing superior chickpea varieties

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

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