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Smyda-Dajmund P, Śliwka J, Janiszewska M, Zimnoch-Guzowska E. Cytoplasmic diversity of potato relatives preserved at Plant Breeding and Acclimatization Institute in Poland. Mol Biol Rep 2020; 47:3929-3935. [PMID: 32406017 PMCID: PMC7239805 DOI: 10.1007/s11033-020-05486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 11/06/2022]
Abstract
Among different types of potato cytoplasmic genomes, some are associated with male sterility or affect agronomic traits. The goal of this study was to analyze types of chloroplast and mitochondrial genomes of selected potato relatives originating from collection of the Institute of Plant Industry, Saint Petersburg, Russia, and preserved in Poland. Using chloroplast and mitochondrial markers the cytoplasm types were determined for 401 genotypes belonging to 43 seed accessions of 28 Solanum species. Among characterized genotypes, 201 (50.1%), 156 (38.9%) and 44 (11%) had cytoplasm types W, D, M, respectively. No accessions with the T, P or A cytoplasm were found. Within cytoplasm W, genotypes with the subtypes: W/α and W/β were identified, but not with W/γ. In S. famatinae, we detected unusual product of the T marker with 65 bp insertion earlier seen exclusively in S. vernei. Among the genotypes of S. leptophyes, two profiles of the ALM_4/ALM_5 marker were observed. S. famatinae and S. vernei come from Argentina, provinces Catamarca and Tucumán. Possibly the insertion in marker T occurred independently in two species, or the accessions were misidentified. Segregation of the ALM_4/ALM_5 marker within S. leptophyes indicates that potato seed accessions are heterogeneous not only due to nuclear DNA polymorphisms but have diversified cytoplasm, too. Our findings are important for exploitation of the tested material in potato breeding. Male-fertile cytoplasm types give a chance of avoiding fertility problems and widening the range of crosses in future generations of breeding materials.
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Affiliation(s)
- Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Marta Janiszewska
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
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Cho KS, Cheon KS, Hong SY, Cho JH, Im JS, Mekapogu M, Yu YS, Park TH. Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. PLANT CELL REPORTS 2016; 35:2113-23. [PMID: 27417695 DOI: 10.1007/s00299-016-2022-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/29/2016] [Indexed: 05/09/2023]
Abstract
Chloroplast genome of Solanum commersonii and S olanum tuberosum were completely sequenced, and Indel markers were successfully applied to distinguish chlorotypes demonstrating the chloroplast genome was randomly distributed during protoplast fusion. Somatic hybridization has been widely employed for the introgression of resistance to several diseases from wild Solanum species to overcome sexual barriers in potato breeding. Solanum commersonii is a major resource used as a parent line in somatic hybridization to improve bacterial wilt resistance in interspecies transfer to cultivated potato (S. tuberosum). Here, we sequenced the complete chloroplast genomes of Lz3.2 (S. commersonii) and S. tuberosum (PT56), which were used to develop fusion products, then compared them with those of five members of the Solanaceae family, S. tuberosum, Capsicum annum, S. lycopersicum, S. bulbocastanum and S. nigrum and Coffea arabica as an out-group. We then developed Indel markers for application in chloroplast genotyping. The complete chloroplast genome of Lz3.2 is composed of 155,525 bp, which is larger than the PT56 genome with 155,296 bp. Gene content, order and orientation of the S. commersonii chloroplast genome were highly conserved with those of other Solanaceae species, and the phylogenetic tree revealed that S. commersonii is located within the same node of S. tuberosum. However, sequence alignment revealed nine Indels between S. commersonii and S. tuberosum in their chloroplast genomes, allowing two Indel markers to be developed. The markers could distinguish the two species and were successfully applied to chloroplast genotyping (chlorotype) in somatic hybrids and their progenies. The results obtained in this study confirmed the random distribution of the chloroplast genome during protoplast fusion and its maternal inheritance and can be applied to select proper plastid genotypes in potato breeding program.
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Affiliation(s)
- Kwang-Soo Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Kyeong-Sik Cheon
- Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Su-Young Hong
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Ji-Hong Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Ju-Seong Im
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Manjulatha Mekapogu
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Yei-Soo Yu
- Phygen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Tae-Ho Park
- Department of Horticulture and Institute of Life and Environment, Daegu University, Gyeongsan, 38453, Republic of Korea.
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Tiwari JK, Devi S, Sundaresha S, Chandel P, Ali N, Singh B, Bhardwaj V, Singh BP. Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum. Genome 2015; 58:305-13. [PMID: 26284309 DOI: 10.1139/gen-2014-0191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Sapna Devi
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - S Sundaresha
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Poonam Chandel
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Nilofer Ali
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Brajesh Singh
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Vinay Bhardwaj
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
| | - Bir Pal Singh
- Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India.,Central Potato Research Institute, Shimla, Himachal Pradesh - 171 001, India
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