Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta, Ramesh; Sankar, Ardith; Sreelakshmi, J; Palle, Gouthami; Leela, C; Rani, Ch. V. Durga; Shankar, V. Gouri; Lavanya, B.; Reddy, P. N.; Dudhe, M. Y.

doi:10.1007/s12298-016-0367-x

Cited by 15 publications

(13 citation statements)

References 31 publications

(37 reference statements)

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“…Firstly, the genetic diversity indices and clustering results showed that the genetic diversity of wild castor materials in South China was poor and low, consistent with the previous reports [17, 19, 20, 23] that recorded a minimum to medium genetic diversity in castor using different kinds of molecular markers. The materials in this experiment were clustered in groups mainly at a genetic distance range of 4.67–5.84, indicating that the wild materials in South China were rich in genetic polymorphism at a low molecular level.…”

Section: Discussionsupporting

confidence: 88%

“…Many molecular markers like SSR (Simple Sequence Repeats), SNP (Single Nucleotide Polymorphism), EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat), AFLP (Amplified Fragment Length Polymorphism), SCOT (Start Codon Targeted Polymorphism), RAPD (Random Amplified Polymorphic DNA), ISSR (Inter-Simple Sequence Repeat) and TRAP ((Target Region Amplification Polymorphism) have been used in assessing the genetic diversity of castor [17–26]. Nonetheless, irrespective of the marker systems used, the global analysis of the genetic diversity of castor germplasm shows the low levels of variability and a lack of geographically structured genetic population [17–19, 23].…”

Section: Introductionmentioning

confidence: 99%

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SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

et al. 2019

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Castor bean is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Currently, castor bean varieties suffer from low productivity and high risk of insect pests and diseases. It is in urgent need to mine elite genes from wild materials for castor breeding. 29 pairs of polymorphic SRAP primers out of 361 pairs were used to analyse the genetic diversity of 473 wild castor materials from South China. 203 bands were amplified by the 29 pairs of primers, of which 169 bands were polymorphic, with a polymorphic percentage of 83.25%. With an average number of alleles per locus (A p ) of 1.801, average number of effective alleles per locus ( A e ) of 1.713 and average percentage of polymorphic loci (P) of 90.04%, these primers were proven to be useful and effective. Nei’ genetic distance between the materials ranged from 1.04 to 25.02, with an average of 13.03. At the genetic distance of 25.02, the materials clustered into two major groups, consistent with the result of population structure analysis. However, more subgroups existed between 5.21 and 13.32. Although not all the materials from the same region were clustered in the same group, an obvious trend existed where the groups were related to regions to a great extent. Based on multiple indices, the genetic diversity of materials from Hainan was the lowest. However, there was not much difference between West Guangdong and Guangxi, although the former was slightly higher. Moderate genetic differentiation was observed in wild materials in South China. The genetic differentiation mainly occurred within population, with maximum differentiation in Guangxi, followed by West Guangdong and the minimum in Hainan. Nonetheless, there was an extensive geneflow between populations. The above results provided a direction for the conservation and breeding application of these materials.

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Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

et al. 2019

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“…The PIC value was varied between 0.386 and 0.88 with an average of 7.4 and shared high genetic diversity (Jia et al 2016). PIC value ranged between 0.27 and 0.49 in Castor (Ricinus communis L), which indicated moderate polymorphism level or genetic diversity in castor genome (Thatikunta et al 2016). The above results indicated that the S. album or other forestry species shows high polymorphism than the agricultural or other crop species.…”

Section: Discussionmentioning

confidence: 84%

“…Likewise, 12 genic SSR markers showed polymorphism in castor genome. The number of alleles was ranged two to three with an average of 2.33 (Thatikunta et al 2016). Genic SSR markers, Farnesyl diphosphate synthase (SaFDS), and Santalene synthase (SaSS) gene expressions were high and characterized as chief genes in regulating heartwood oil biosynthesis in S. album (Rani et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Assessment of morphological and genetic variability through genic microsatellite markers for essential oil in Sandalwood (Santalum album L.)

et al. 2019

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Sandalwood (Santalum album L; family Santalaceae) is a highly significant aromatic oil yielding tree. It is valued for two important traits, heartwood and essential oil obtained from the heartwood. This study was proposed to assess the morphological and genetic variability of sandalwood accessions. For this, genotypes were randomly selected (n = 177) from the 14 populations from three states in southern India. The total heartwood oil content and quality was estimated by UV method and GC-MS. Total 14 oil-specific genic SSR markers were procured to evaluate the genetic diversity among the sandalwood accessions. Total core size, heartwood content, and oil of S. album ranged from 4.4 to 19.1 cm; 0.0 to 17.3 cm; and 0.0 to 5.96% with covariance 27.61, 85.25, and 73.12% followed by mean 9.74, 3.77, and 2.71, respectively. Genetic diversity estimates were highly polymorphic in terms of Na 7.28, Ne 5.89, He 8.0 PIC 0.891, with little Ho, and F-0.922. AMOVA revealed that minimal genetic variation among populations and highest variation was found among individuals with Nm (58.4). The UPGMA reveals the cluster favored the grouping pattern by the PCA analysis. Structure and PCA analysis clustered the entire populations into two major groups with F ST 0.046 in which population of Kerala and Karnataka were pure and Telangana accessions were found admixtures. No significant correlation (r 2 = 0.23, P = 0.00) was observed between heartwood oil and genetic structures. A high degree of transferability of genic markers would facilitate the assessment of novel genotypes for future tree improvement and conservation of Sandalwood populations.

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“…Similar in silico approaches in EST-SSR marker development were performed by other studies focusing on other plants, such as bamboo (Cai et al, 2019), mint (Kumar et al, 2015), castor (Thatikunta et al, 2016), Ethiopian potato (Gadissa et al, 2018) and Elymus species (Zhang et al, 2019). The EST-derived SSR markers generated in this study can be used for functional analysis of R genes, once verified by wet lab experiments.…”

Section: Resultsmentioning

confidence: 91%

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Lantican

Cortaga

Manohar

et al. 2020

Preprint

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10Plants have developed mechanisms to recognize pathogen and insect attacks and to 11 activate defense response against them through the action of resistance genes (R genes). 12Hence, R gene analogs (RGAs) have been widely studied and efficiently used for breeding of 13 resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, 14 is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from 15 different varieties were identified and characterized via de novo assembly of raw transcriptome 16 sequences currently available in biological repositories. Using bioinformatics pipelines, a core 17 RGA database of mango with 747 protein models was established and were classified based 18 on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide 19 binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 20 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 21 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like 22 proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein 23 (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly 24 clustered the core RGAs into 6 major clades based on their domain classification, while TM- 25CC formed subclades all across the tree. The phylogenetic results suggest highly divergent 26 functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms 27 race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their 29 expression profiles across different mango varieties were also determined. From the mango 30 RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed 31 targeting these potential markers. To date, this is the most comprehensive analysis of mango 32 RGAs which offer a trove of markers for direct utilization in resistance breeding of mango. 33 34 35 36 Introduction 37 Mango (Mangifera indica L.) is a globally popular fruit crop with economical and 38 agricultural significance, especially in the (sub)tropics where it is largely cultivated. One of the 39 constraints in mango production worldwide include a myriad of insect pests (e.g., oriental fruit 40 fly, mango hopper, cecid fly, etc.) and diseases, (e.g., anthracnose, stem-end rot, scab, etc.) 41 which can affect mango at different life stages thus significantly reducing fruit quality and yield 42 (Bally, 2006). These are major barriers to the export market and can impede international 43 trade as many pests and diseases in mango are important quarantine considerations. 44 Along the course of evolution, plants have generally developed mechanisms to 45 recognize pathogen and insect attacks and to activate defense response against them (Dangl 46 and Jones., 2001; Acevedo et al., 2015). The mole...

show abstract

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Cited by 15 publications

References 31 publications

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

Assessment of morphological and genetic variability through genic microsatellite markers for essential oil in Sandalwood (Santalum album L.)

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

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