Screening, selection and real-time qPCR validation for phytoplasma resistance in sesame (Sesamum indicum L.)

Ustun, Rustem; Yol, Engin; İkten, Cengiz; Catal, Mursel; Uzun, Bülent

doi:10.1007/s10681-017-1936-y

Cited by 15 publications

(6 citation statements)

References 19 publications

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“…The Mediterranean sesame core collection has useful characteristics, such as high yield [15], high oil content [39], and high phyllody resistance [40]. The SNPs obtained from this collection could benefit future breeding and association mapping work in sesame.…”

Section: Discussionmentioning

confidence: 99%

“…In sesame, the Mediterranean sesame core collection has been selected using a principal component score strategy from a worldwide sesame collection [15] that includes 345 genotypes representing 29 sesame-growing countries. This core collection contains high-yielding genotypes as well as those with commercially important traits, such as different seed colors, early flowering, adaptability [15], high oil content [39], and phyllody resistance [40]. Evaluation of the genetic variation and differentiation of genotypes in this collection at the genomic level will allow a more effective use of these valuable genetic resources to exploit new alleles that could be exploited in breeding programs to enhance the productivity of sesame.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

2019

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The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

2019

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“…This could be the main reason for the weakened seed and oil yield and could contribute to the attributes of phytoplasma-infected sesame crop plants. Other reasons could include the flower deformation (abnormal zygomorphic flowers forming instead of normal actinomorphic flowers), the irreversible loss of flower fertility, and the presence of seedless capsules induced by hormonal imbalance and the damage caused by the effectors secreted by pathogenic phytoplasma cells [76]. However, most seeds in diseased plants are small (seed index; Table 5) due to their slow phenological development at the post-blooming stage.…”

Section: Discussionmentioning

confidence: 99%

Effect of Phytoplasma Associated with Sesame Phyllody on Ultrastructural Modification, Physio-Biochemical Traits, Productivity and Oil Quality

Ahmed

Farrag

Kheder

et al. 2022

Plants

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Phytoplasmas are obligate cell-wall-less plant pathogenic bacteria that infect many economically important crops, causing considerable yield losses worldwide. Very little information is known about phytoplasma–host plant interaction mechanisms and their influence on sesame yield and oil quality. Therefore, our aim was to explore the ultrastructural and agro-physio-biochemical responses of sesame plants and their effects on sesame productivity and oil quality in response to phytoplasma infection. Sesame leaf samples exhibiting phyllody symptoms were collected from three experimental fields during the 2021 growing season. Phytoplasma was successfully detected by nested- polymerase chain reaction (PCR) assays using the universal primer pairs P1/P7 and R16F2n/R16R2, and the product of approximately 1200 bp was amplified. The amplified product of 16S rRNA was sequenced and compared with other available phytoplasma’s 16S rRNA in the GenBank database. Phylogenetic analysis revealed that our Egyptian isolate under accession number MW945416 is closely related to the 16SrII group and showed close (99.7%) identity with MH011394 and L33765.1, which were isolated from Egypt and the USA, respectively. The microscopic examination of phytoplasma-infected plants revealed an observable deterioration in tissue and cell ultrastructure. The primary and secondary metabolites considerably increased in infected plants compared with healthy ones. Moreover, phytoplasma-infected plants showed drastically reduced water content, chlorophyll content, growth, and yield components, resulting in 37.9% and 42.5% reductions in seed and oil yield, respectively. The peroxide value of the infected plant’s oil was 43.2% higher than that of healthy ones, suggesting a short shelf-life. Our findings will provide a better understanding of the phyllody disease pathosystem, helping us to develop effective strategies for overcoming such diseases.

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“…Sesame plants grow well in tropical and subtropical climates, can tolerate low soil moisture, require low labor input, and can be grown in pure or mixed stands with diverse crops [ 9 ]. Despite these advantages, sesame yield is very low due to the persistence of wild-type traits—nonsynchronous flowering, capsule shattering in harvest [ 10 ], susceptibility to phyllody disease [ 11 ], indeterminate growth [ 12 ], late maturation, and low environmental adaptability [ 13 , 14 ]. The paucity of genetic diversity in sesame species, in addition to the limited amount of basic research, breeding studies, and international cooperation, have hindered efforts to improve agronomically important traits in sesame species.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

Kizil

Basak

Guden

et al. 2020

Plants

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The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1–2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3′- and 5′- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.

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Screening, selection and real-time qPCR validation for phytoplasma resistance in sesame (Sesamum indicum L.)

Cited by 15 publications

References 19 publications

Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

Effect of Phytoplasma Associated with Sesame Phyllody on Ultrastructural Modification, Physio-Biochemical Traits, Productivity and Oil Quality

Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

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