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Twenty-two wild potato (Solanum) species were used for SSR analysis. Due to space limitation on the image panel, accessions are mentioned here: Solanum acaule (CGN17938), S. berthaultii (PI 265858), S. cardiophyllum (PI 283062), S. chacoense (PI 197760), S. chomatophilum (PI 310990), S. hannemanii (CGN18001), S. hjertingii (PI 283103), S. hougasii (PI 161727), S. huancabambense
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Allelic variation in wild potato (Solanum) species was analysed using 14 simple sequence repeat (SSR) markers. SSR allelic profiles showed high polymorphism and distinctness among the wild species. A total of 109 alleles of 14 polymorphic SSR markers were scored in 82 accessions belonging to 22 wild potato species. Allele size ranged from a minimum...
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... were obtained from the international gene banks namely Potato Introduction Station, NRSP-6, Sturgeon Bay, Wisconsin (USA); Centre for Genetic Resources, Wageningen University and Research, the Netherlands (CGN); and International Potato Centre, Lima, Peru. A brief description of the wild species is summarised in Table 1 and images are shown in Fig. ...
Context 2
... the wild species that originated from South American countries like Argentina (S. acaule, S. chacoense, S. hannemanii, S. microdontum and S. vernei) and Peru (S. chomatophilum, S. huancabambense and S. medians) have been grouped into cluster I. On the Table 2 Molecular profiling of wild potato species by SSR markers. SSR markers source: Ghislain et al. (2009) (#1-12) and Provan et al. (1996) (#13-14) PIC polymorphic information content, T a annealing temperature a All SSR amplified at single locus except, STM019 amplifies at two loci ( Ghislain et al. 2009 Fig. 2 Diversity analysis of 82 accessions belonging to 22 wild species using 14 SSR markers based on the Dice coefficient using the weighted neighbour-joining tree construction method. Bootstrap values are shown on the nodes. ...
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Citations
... (A) Illustration of S. iopetalum(Correll 1962). (B) Plant shape of S. iopetalum(Tiwari et al. 2019). IOP is the three letter abbreviation for S. iopetalum. ...
Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes (S. tuberosum) and is closely related to Mexican Solanum species (S. stoloniferum, S. verrucosum, S. hougasii, S. hjertingii, and S. demissum). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.
... Nowadays, a potato genetic identification (PGI) kit is also available, which contains 24 highly polymorphic SSR markers [17,18]. The SSR markers from this kit and from some other studies were extensively used to study the genetic diversity in different potato populations [15,16,[19][20][21][22]. The aim of the present study was to evaluate the allelic variations in a highly diverse potato germplasm consisting of 353 potato accessions by 25 SSR markers to study the molecular diversity and to generate an SSR allelic dataset for potato breeding. ...
... They reported a lower PIC value compared to the current findings. A similar range of PIC values (0.66 to 0.91) has been reported by Tiwari et al. [22] in the wild potato species with 14 SSRs in a population of 82 potato accessions. The SSRs are useful to differentiate the closely related taxa of potato [31]. ...
... The findings of this study suggest that SSR markers are efficient to examine the genetic diversity in the potato diversity panel. These findings are in agreement with the results of previous studies conducted to evaluate the genetic diversity in different potato germplasms [15,16,[19][20][21][22]. The SSR markers, due to their desirable characteristics, such as their simplicity, abundance, codominant nature, extensive coverage on the genome, high reproducibility, and polymorphism, are considered as ideal molecular markers for diversity analysis, varietal identification, phylogenetic studies, and germplasm characterization and conservation [14,34,35]. ...
The allelic variations in a diversity panel of 353 potato accessions, including 256 accessions belonging to Solanum tuberosum sub spp. tuberosum, 49 accessions belonging to Solanum tuberosum sub spp. andigena, and 48 Indian potato varieties were analysed using 25 simple sequence repeat (SSR) markers. The SSR allelic profiles revealed high levels of polymorphism and distinctness among the accessions studied. A total of 343 alleles of 25 SSR markers were observed in the diversity panel of 353 highly diverse tetraploid potato accessions. The number of alleles produced per SSR varied from 8 for the marker STM1053 to 25 for the marker STIKA. The polymorphic information content (PIC) ranged from 0.66 (STG0010) to 0.93 (STM1106) with an average of 0.82. The cluster analysis using the SSR allelic profiles of 353 accessions divided the population into five major groups. The association mapping for late blight resistance identified six markers with the general linear model (GLM), and out of these six markers significance of three markers was reconfirmed with the mixed linear model (MLM). The findings of this study suggest that SSRs are the appropriate markers for evaluating genetic diversity and population structure within different potato germplasm collections. A significant diversity across the tetraploid potato accessions was observed. Moreover, the markers identified in this study could be useful in marker-assisted selection (MAS) breeding in potato for late blight resistance (LBR).
... , varietal identification, and characterization of 82 accessions of 22 wild potato species by 14 SSR for uncovering traits of biotic and abiotic resistance such as late blight resistance.Tiwari et al. (2019) 217 cultivars in the Chinese breeding program were efficiently characterized by 11 SSR markers with an average PIC of 0.83Duan et al. (2019) ...
Potato (Solanum tuberosum L.) is an essential ingredient of the human diet in many countries. It is considered one of the top promising crops to reduce human hunger and poverty in the world. As a staple, it is the third most-produced food crop in the world. First domesticated in the mountains of South America, nowadays potato is cultivated worldwide in 159 countries. Cultivated potato (S. tuberosum L.) and its wild relatives belong to the Solanum sect. Petota (Solanaceae), which includes approximately 110 Solanum species. The large genetic diversity in the Solanaceae can be used in potato breeding for the development of new elite varieties that are more yielding, nutritious, and resilient to environmental stresses. Many studies have investigated the germplasm diversity of wild potato relatives in the center of origin. This chapter summarizes the studies done on potato germplasm diversity in terms of agro-morphological, molecular characterization, and preservation.
... SSR has been used to analyze genetic diversity within wild species showing noteworthy resistances to R. solanacearum and aphids. A new set of 24 highly informative SSR markers (two from each linkage group) named as the Potato Genome Identification (PGI) kit has been used worldwide in potato varieties (Tiwari et al. 2018a) and wild species (Tiwari et al. 2019). The role of cytoplasmic markers (T/β, W/α, W/γ and A/ε) has also been studied in potato using plastome-and chondriome-specific markers (Tiwari et al. 2014). ...
Potato is a globally important food crop. In addition to various other factors, potato suffers from many biotic stresses. The important diseases are late blight, viruses, bacterial wilt, bacterial soft rot, dry rot, charcoal rot, common scab, black scurf and wart; and insect-pests are like aphid, whitefly, mite, potato tuber moth, potato cyst nematode, potato leaf hopper and white grub. Of which, late blight is the most devastating disease, whereas aphids and whiteflies are more important pests. These biotic factors limit crop growth and reduce tuber yields. The genus Solanum is one of richest source of genetic diversity and provides great opportunities for genetic enhancement of potato applying classical genetics, traditional breeding and modern genomics tools. With the available knowledge on potato genetic resources, genetic diversity, molecular markers, mapping, gene tagging, marker-assisted selection and high-resolution maps, there had been a considerable advancement in potato. The availability of the potato genome sequence and recently sequenced some more wild species, next-generation breeding tools like genome editing, high-throughput genotyping using single nucleotide polymorphism array and genotyping by sequencing, phenomics, genome wide association mapping, genomic selection and other omics resources further provide tremendous opportunities for next-generation breeding of potato. This chapter highlights on genomic designing for biotic stress resistance in potato.KeywordsBiotic stressGenetic diversityBreedingGenomicsPotato
... SSR has been used to analyze genetic diversity within wild species showing noteworthy resistances to R. solanacearum and aphids. A new set of 24 highly informative SSR markers (two from each linkage group) named as the Potato Genome Identification (PGI) kit has been used worldwide in potato varieties (Tiwari et al. 2018a) and wild species (Tiwari et al. 2019). The role of cytoplasmic markers (T/β, W/α, W/γ and A/ε) has also been studied in potato using plastome-and chondriome-specific markers (Tiwari et al. 2014). ...
Potato is a globally important food crop. In addition to various other
factors, potato suffers from many biotic stresses. The important diseases are late
blight, viruses, bacterial wilt, bacterial soft rot, dry rot, charcoal rot, common scab,
black scurf andwart; and insect-pests are like aphid, whitefly,mite, potato tuber moth,
potato cyst nematode, potato leaf hopper and white grub. Of which, late blight is the
most devastating disease, whereas aphids and whiteflies are more important pests.
These biotic factors limit crop growth and reduce tuber yields. The genus Solanum is
one of richest source of genetic diversity and provides great opportunities for genetic
enhancement of potato applying classical genetics, traditional breeding and modern
genomics tools. With the available knowledge on potato genetic resources, genetic
diversity, molecular markers, mapping, gene tagging, marker-assisted selection and
high-resolution maps, there had been a considerable advancement in potato. The
availability of the potato genome sequence and recently sequenced some more wild
species, next-generation breeding tools like genome editing, high-throughput genotyping
using single nucleotide polymorphism array and genotyping by sequencing,
phenomics, genome wide association mapping, genomic selection and other omics
resources further provide tremendous opportunities for next-generation breeding of
potato. This chapter highlights on genomic designing for biotic stress resistance in
potato.
... Among several molecular markers, SSR is an easy-to-use, reproducible, locus-specific, co-dominance and highly polymorphic in nature (Provan et al. 1996). SSR markers have been used in potato for various applications; like molecular characterization of cultivated/semi-cultivated/ wild potato species (Ghislain et al. 2009), wild species (Tiwari et al. 2019), somatic hybrids (Chandel et al. 2015), varietal identification (Tiwari et al. 2018a), and genetic diversity (Provan et al. 1996). Hence, the aim of this study was to develop diagnostic SSR markers for identification of advance stage potato hybrids/progenies developed using interspecific somatic hybrids and common potato varieties. ...
The aim of present study was to identify simple sequence repeat (SSR) markers linked to potato somatic hybrid progenies. A total of 50 breeding lines (parents and progenies) were analyzed using 59 simple sequence repeat (SSR) markers. Of which, SSR marker STM0003 clearly distinguished the parents i.e. somatic hybrid P8 (Solanum tuberosum dihaploid C-13 + wild species S. pinnatisectum) and potato cv. Kufri Jyoti, and their progenies (MSH-14/112, MSH-14/113, MSH-14/114, MSH-14/115, MSH-14/116, MSH-14/122 and MSH-14/123). STM0003 showed three distinct alleles (103, 132 and 144 bp), where both P8 and progenies contained 103 and 144 bp, and Kufri Jyoti had 132 and 144 bp alleles. On the other hand, STI0001 distinguished progenies namely MSH/17-16 (Kufri Garima × Crd10), MSH/17-25 (Kufri Garima × P10) and MSH/17- 27 (Kufri Jyoti × Crd 16) with respect to their parents, and STI0001 contained six alleles (169, 172, 175, 178, 184 and 188 bp). The study suggests that STM0003 and STI0001 are diagnostic markers to identify these somatic hybrid derived progenies and parents.
... Among them, simple sequence repeat (SSR) is easy-to-use, reproducible, locus-specific, co-dominant and polymorphic (Provan et al. 1996). Numerous researchers have used SSR in characterization of potato species (Ghislain et al. 2009), somatic hybrids (Chandel et al. 2015), varietal identification (Tiwari et al. 2018a), wild species (Tiwari et al. 2019) and genetic diversity (Provan et al. 1996). Hence, the aim of this study was to carry out DNA fingerprinting of hybrid progenies of different potatoes (multi-coloured flesh hybrids and interspecific somatic hybrids) by SSR markers for clonal identity and genetic fidelity purpose. ...
... Interspecific potato somatic hybrids TIWARI ET AL. Scoring and data analysis: All reactions were repeated twice and distinct SSR peaks were scored for 165 genotypes and analysed as described by Tiwari et al. (2019). Briefly, a datasheet was prepared in the form of presence (1) and absence (0) of SSR alleles. ...
... These results support findings of SSR analysis in potato by various workers. Previously, we have well-characterized these markers in allelic profiling of potato varieties and wild species, and also for genetic fidelity testing of in vitro propagated plants (Tiwari et al. 2018a(Tiwari et al. , 2019. Many SSR markers have been applied in characterization of potato germplasm (Ghislain et al. 2009, Provan et al. 1996, Indian potato varieties (Tiwari et al. 2018a), wild potato species (Tiwari et al. 2019), Andigena core collection, somatic hybrids (Chandel et al. 2015). ...
The objective of this study was to develop SSR profiles of potato (Solanum tuberosum L.) hybrids for genetic fidelity purpose. The multi-coloured flesh potato hybrids and interspecific somatic hybrids-derived progenies were for the study conducted at ICAR-CPRI, Shimla during 2019–20. A total of 165 potato genotypes were analysed using two well-known potato SSR markers (STU6SNRN and STIIKA). High polymorphism was observed in STIIKA (PIC: 0.93) than STU6SNRN (PIC: 0.82), and higher number of alleles were observed in STIIKA (23) than STU6SNRN (7). In STU6SNRN, alleles size 174, 179, 182, 190 and 200 bp were predominant whereas in STIIKA, alleles size 191, 195, 198, 201, 221, 223, 231, 242, 245 and 256 were observed frequently in more than 50% of the genotypes.
Diversity analysis showed a clear distinction among the genotypes based on the Jaccard dissimilarity coefficient by the Neighbour-joining tree method using the DARwin software. SSR fingerprints would be valuable resources to strengthen genetic fidelity of these hybrids and identification of true-to-type clones.
... This approach can be used for more species with sufficient transcriptome data. Numerous new SSR loci with polymorphisms in various species will be found and some research concerning microsatellites may be extended with the data support, for instance, the distribution rules and structural features of SSRs with polymorphisms in functional regions of genes, the influences of external environment on SSR mutations, and characteristics of SSR alleles among different species [54][55][56]. Moreover, examining the vast new loci among diverse species might be valuable to researchers studying the laws of SSR mutations during biological evolution [57]. ...
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.
The diversity of native potatoes cultivated above 3500 masl in the Pasco region (Central Andes of Peru) has not been fully characterized. It is currently subject to constant genetic erosion caused by biotic and abiotic factors. The research aimed to characterize phenotypically and genotypically 40 native potato landraces representative of 4 Solanum species. Twenty phenotypic descriptors and 10 microsatellites were used for genetic evaluation. Likewise, the ploidy level was evaluated based on the number of chloroplasts in the stomata. The clustering analysis was performed using the Infostat software and the R program with the Adegenet and Polysat libraries. The phenotypic characterization allowed to obtain five groups with a distance coefficient of 9.5. The molecular characterization found seven groups and 58 alleles in total. The average number of alleles per microsatellite was 5.5. 13.2 % of duplicates were identified. The microsatellites STG001, STM1106, ST0032, and STM5127 with an average He of 0.8 and a polymorphism information content (PIC) of 0.5 - 0.8 were the most informative. Finally, the ploidy results were 13 % diploid, 35 % triploid, and 52 % tetraploid. It was evidenced low diversity when using a set of 10 SSR markers, which indicates limited applicability for studying the genetic diversity of local potato landraces. It is necessary to involve a broader range of markers and a more diverse set of genotypes from the Pasco region for further studies.
Native potatoes are an important source of biotic/abiotic resistance and quality traits improvement. The aim of this study was to analyse genetic diversity and population structure using 14 simple sequence repeat (SSR) markers and 51 distinctness, uniformity and novelty (DUS) phenotypic traits in native potato collection (94 accessions) in India representing sub-tropical plains (45), north-west (NW) hills (25), north-east (NE) hills (22) and two unknown sources. Polymorphic 14 SSR loci revealed 97 alleles, where allele sizes per marker ranged between 75 bp (STM0037) and 296 bp (STM5114), and the number of alleles per marker varied between 2 (STI0030) and 13 (STPoAc58/STM0031). The polymorphic information content (PIC) of SSR was found between 0.29 (STI0030) and 0.90 (STPoAc58/STM0031). The accessions were grouped into four major clusters using both SSR and phenotypic traits separately based on the Jaccard similarity coefficient using the neighbour-joining clustering approach by the DARWin software. However, both clusters contained different accessions and intermixing was observed amongst collection sources. Clusters were supported by principal component analysis (PCA) plots based on both SSR and phenotypic data. Population structure analysis revealed four populations using the SRUCTURE software based on the SSR data. Taken together, our study suggests that SSR and DUS trait profiling are the key components of genetic diversity and population structure analysis in the potato. This would be useful for genetic fidelity testing of true-to-type accessions in future.
