Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

Srivastava, Ram; Bajaj, Deepak; Sayal, Yogesh K.; Meher, Prabina Kumar; Upadhyaya, Hari D.; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Rao, Atmakuri Ramakrishna; Parida, Swarup K.

doi:10.1016/j.plantsci.2016.08.013

Cited by 12 publications

(7 citation statements)

References 79 publications

(122 reference statements)

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“…Among the simple PCR-based markers, ILP is gene-specific, often hypervariable, neutral to the environment, and co-dominant, which has a high transferability rate in related species 12 . Previously, genome-wide intron-derived polymorphic markers in rice 14 , foxtail millet 15 sorghum 26 , chickpea 27 , and Macrotyloma spp 28 were reported. In the present study, we developed a large number of CsILP markers (4192) from the two sequenced genomes of tea harnessing the intron derived marker development tool 12 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Rohilla

Mazumder

Saha

et al. 2022

Sci Rep

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Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Rohilla

Mazumder

Saha

et al. 2022

Sci Rep

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“…As illustrated by the Circos graph, 8,812 PIP primers (targeted 3,445 genes) were scattered evenly across all of the 8 Tunisia chromosomes. In chickpea, 7,454 intron-spanning markers (ISMs) were developed from introns of 3,283 genes representing the entire eight chromosomes (Srivastava et al, 2016 ). Badoni et al ( 2016 ) also developed 16,510 ILP markers, which were physically mapped on 12 chromosomes, and found them to be well-distributed throughout the rice genome.…”

Section: Discussionmentioning

confidence: 99%

Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate

et al. 2022

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Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron polymorphism (PIP) markers specific to 3,445 (13.40%) gene models that span 8 Tunisia chromosomes. The ePCR validation of all these PIP markers on the Tunisia genome revealed single-locus amplification for 1,233 (14%) markers corresponding to 958 (27.80%) genes. The markers yielding single amplicons were then mapped onto Tunisia chromosomes to develop a saturated linkage map. The functional categorization of 958 genes revealed them to be a part of the nucleus and the cytoplasm having protein binding and catalytic activity, and these genes are mainly involved in the metabolic process, including photosynthesis. Further, through ePCR, 1,233 PIP markers were assayed on multiple genomes, which resulted in the identification of 886 polymorphic markers with an average PIC value of 0.62. In silico comparative mapping based on physically mapped PIP markers indicates a higher synteny of Tunisia with the Dabenzi and Taishanhong genomes (>98%) in comparison with the AG2017 genome (95%). We then performed experimental validation of a subset of 100 PIP primers on eight pomegranate genotypes and identified 76 polymorphic markers, with 15 having PIC values ≥0.50. We demonstrated the potential utility of the developed markers by analyzing the genetic diversity of 31 pomegranate genotypes using 24 PIP markers. This study reports for the first time large-scale development of gene-based and chromosome-specific PIP markers, which would serve as a rich marker resource for genetic variation studies, functional gene discovery, and genomics-assisted breeding of pomegranate.

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“…Following the availability of the whole genome assemblies, researchers have developed several databases to catalogue genome-wide DNA markers for applications in research and breeding such as chickpea microsatellite database (CicArMiSatDB) (Doddamani et al 2014) and Microsatellite Database (CMsDB) (Parida et al 2015). Other databases on chickpea genomic resources include CicArVarDB encompassing SNP and InDel (Doddamani et al 2015), and ISM-ILP database (Srivastava et al 2016) that provides information on 119,169 and 110,491 ISMs from protein-coding genes desi (23,129) and kabuli (20,386) chickpeas.…”

Section: Chickpeamentioning

confidence: 99%

Next generation breeding in pulses: Present status and future directions

Kumar

Mir

Sharma

et al. 2021

Crop Breed. Appl. Biotechnol.

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Human population growth in combination with changing patterns of global food consumption under climate change is posing formidable challenge to attaining sustainable global food security. Besides being economically viable sources of plant based protein for human consumption, pulses are also beneficial for the environment owing to their inherent capacity of nitrogen fixation. Hence, further development of pulses has become imperative in the vigorously transitional global scenario where flourishing anthropogenic activities are triggering irreplaceable depletion of natural resources. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources in pulse crops including high-throughput DNA markers, candidate gene(s) and QTLs for predicting plant phenotypes, and whole genome sequences. With refinements in DNA sequencing technologies and computational analytical tools, the rapidly grown numbers of sequenced pulse genomes offer novel insights on crop evolution and breeding history.Integration of new-generation genomic and phenomic tools with generation acceleration procedures like genomic selection and speed breeding could greatly accelerate progress in pulses genetic improvement. The present review discusses current status and future scope of using next-generation breeding approaches in pulses that will cause not only an increase in the rate of developing climateresilient superior cultivars but also help to reach to goal of global food security.

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Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

Cited by 12 publications

References 79 publications

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate

Next generation breeding in pulses: Present status and future directions

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