Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

Thudi, Mahendar; Chen, Yinglong; Pang, Jiayin; Kalavikatte, Danamma; Bajaj, Prasad; Roorkiwal, Manish; Chitikineni, Annapurna; Ryan, Megan H.; Lambers, Hans; Siddique, Kadambot H. M.; Varshney, Rajeev K.

doi:10.3389/fpls.2021.636973

Cited by 21 publications

(12 citation statements)

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“…Technological advances in next-generation sequencing-based genotyping technologies have enabled GWAS to be used routinely in crop genetics research (Song et al 2016 ; Cao et al 2019 ). Several studies have demonstrated the efficiency of GWAS to identify marker-trait associations (MTAs) regulating important agronomic traits and to detect the underlying putative genes in different plant species such as Arabidopsis thaliana (Ren et al 2019 ), rice (Xu and Crouch 2008 ; Li et al 2014 ), maize (Yang and Zhu 2005 ), wheat (Wang et al 1999 ), cotton (Lai et al 2016 ), soybean (Hyten et al 2008 ; Cao et al 2017 ; Fang et al 2017 ; Li et al 2017 ; Chang et al 2018 ), chickpea (Varshney et al 2019a , b ; Thudi et al 2021 ), pigeonpea (Varshney et al 2017a , b ), and pearl millet (Varshney et al 2017a , b ).…”

Section: Introductionmentioning

confidence: 99%

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean

et al. 2022

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Key message Plant height of soybean is associated with a haplotype block on chromosome 19, which classified 211 soybean accessions into five distinct groups showing significant differences for the target trait. Abstract Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height.

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Section: Introductionmentioning

confidence: 99%

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean

et al. 2022

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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%

“…Population stratification has been established in the chickpea reference set ( Thudi et al, 2021 ), with three clusters/subpopulations independent of biological status and seed type. In the present study, we detected three subpopulations with ADMIXTURE in the reference set, including 258 accessions.…”

Section: Discussionmentioning

confidence: 99%

“…restricted allelic diversity and limited genetic resolution; Brachi et al, 2011 ; 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 ).…”

Section: Discussionmentioning

confidence: 99%

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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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“…Besides the above-mentioned reports, GWAS has also been conducted for yield and related traits in chickpea (Li et al, 2021), root morphological traits (Thudi et al, 2021), nutrient content (Diapari et al, 2014;Sab et al, 2020) and abiotic tolerance traits (Thudi et al, 2014;Samineni et al, 2022). Thus, the associated genomic regions identified through GWAS could be used for breeding programs to improve yield-related traits, nutrient content, and biotic and abiotic stress tolerance in chickpea.…”

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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Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

Cited by 21 publications

References 60 publications

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean

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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