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פותח על ידי קלירמאש פתרונות בע"מ -
Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Year:
2015
Source of publication :
BMC Plant Biology
Authors :
אופיר, רון
;
.
איש-שלום, מזל
;
.
אשד, רוית
;
.
בניטה, מירי
;
.
כהן, יובל
;
.
סעדה, דוד
;
.
רובינשטיין, מור
;
.
רוזן, עדה
;
.
שרמן, עמיר
;
.
Volume :
15
Co-Authors:
Sherman, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Rubinstein, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Eshed, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Benita, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Ish-Shalom, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Sharabi-Schwager, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
Rozen, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Saada, D., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Cohen, Y., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Ophir, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Facilitators :
From page:
0
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0
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Total pages:
1
)
Abstract:
Background: Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. Results: We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1 %) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5 % were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: One group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS = -0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST = 0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. Conclusions: Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity. © 2015 Sherman et al.
Note:
Related Files :
Genetics
Israel
mango
metabolism
molecular genetics
Molecular Sequence Data
sequence analysis
עוד תגיות
תוכן קשור
More details
DOI :
10.1186/s12870-015-0663-6
Article number:
277
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
30495
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 00:55
Scientific Publication
Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
15
Sherman, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Rubinstein, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Eshed, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Benita, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Ish-Shalom, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Sharabi-Schwager, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
Rozen, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Saada, D., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Cohen, Y., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Ophir, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Background: Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. Results: We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1 %) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5 % were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: One group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS = -0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST = 0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. Conclusions: Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity. © 2015 Sherman et al.
Scientific Publication
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