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ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China Full text
2014
ZHANG Kai, WU Zheng-dan, LI Yan-hua, ZHANG Han, WANG Liang-ping, ZHOU Quan-lu, TANG Dao-bin, FU Yu-fan, HE Feng-fa, JIANG Yu-chun, YANG Hang , WANG Ji-chun (1State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, P.R.China 2Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Ji’nan 250100, P.R.China 3Shandong Rice Research Institute, Ji’nan 250100, P.R.China)
ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China Full text
2014
ZHANG Kai, WU Zheng-dan, LI Yan-hua, ZHANG Han, WANG Liang-ping, ZHOU Quan-lu, TANG Dao-bin, FU Yu-fan, HE Feng-fa, JIANG Yu-chun, YANG Hang , WANG Ji-chun (1State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, P.R.China 2Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Ji’nan 250100, P.R.China 3Shandong Rice Research Institute, Ji’nan 250100, P.R.China)
To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat (ISSR) markers. The mean genetic similarity coefficient, Nei’s gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and five subpopulations based on neighbor-joining (NJ) clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identified. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to flesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance (AMOVA) revealed small but significant difference between white and orange-fleshed sweet potato accessions. Small but significant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.
Show more [+] Less [-]ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China Full text
2014
Zhang, Kai | WU, Zheng-dan | LI, Yan-hua | Zhang, Han | WANG, Liang-ping | ZHOU, Quan-lu | TANG, Dao-bin | FU, Yu-fan | HE, Feng-fa | JIANG, Yu-chun | YANG, Hang | WANG, Ji-chun
To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat (ISSR) markers. The mean genetic similarity coefficient, Nei's gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and five subpopulations based on neighbor-joining (NJ) clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identified. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to flesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance (AMOVA) revealed small but significant difference between white and orange-fleshed sweet potato accessions. Small but significant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.
Show more [+] Less [-]ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China Full text
2014
Kai ZHANG | Zheng-dan WU | Yan-hua LI | Han ZHANG | Liang-ping WANG | Quan-lu ZHOU | Dao-bin TANG | Yu-fan FU | Feng-fa HE | Yu-chun JIANG | Hang YANG | Ji-chun WANG
To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat (ISSR) markers. The mean genetic similarity coefficient, Nei's gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and five subpopulations based on neighbor-joining (NJ) clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identified. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to flesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance (AMOVA) revealed small but significant difference between white and orange-fleshed sweet potato accessions. Small but significant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.
Show more [+] Less [-]Using SSR to Evaluate the Genetic Diversity of Potato Cultivars from Yunnan Province (SW China) Full text
2014
Liao, Hong | Guo, Huachun
The genetic diversity of potato cultivars collected from Yunnan Province was evaluated using 24 pairs of SSR markers. SSR analysis of 24 pairs of primers showed varying degrees of polymorphism among the 85 cultivars: 297 of the 304 bands were polymorphic. The primers yielded between 5 (STM2028) and 19 (StI029) bands (mean 12). The ratio of polymorphic bands ranged from 83.33% to 100% (mean 97.75%). Polymorphism information content (PIC) varied from 69.31% to 93.67% (mean 86.47%). Genetic similarity ranged from 0.5987 to 0.7632, indicating relatively low genetic diversity in the potato cultivars from Yunnan Province. Cluster analysis by UPGMA and PCA clearly delineated the genetic relationships of all cultivars; 83 of the 85 cultivars could be discriminated by only two pairs of primers, STM0030 and STM1104. The high polymorphism and good resolution of the primers used in this study make them good tools for discriminating potato cultivars.
Show more [+] Less [-]Characterization of the genetic diversity of Uganda?s sweet potato (Ipomoea batatas) germplasm using microsatellites markers Full text
2014
barbara m. zawedde | geovani b. amaro | rebecca grumet | jim hancock | marc ghislain | eric magembe
Barbara M. Zawedde et al., 'Characterization of the genetic diversity of Uganda?s sweet potato (Ipomoea batatas) germplasm using microsatellites markers', Genetic Resources and Crop Evolution, vol. 62(4), pp.501-513, Springer Nature, 2014
Show more [+] Less [-]Vegetative compatibility and rep-PCR DNA fingerprinting groups of Fusarium solani isolates obtained from different hosts and their pathogenicity Full text
2014
Fallahi, M. | Javan-Nikkhah, M. | Fotouhifar, Kh. B. | Moradzadeh Eskandari, M.
Fusarium solain is the most important pathogen of huge range of plant hosts, especially potato in the word, which causes tuber rot in storage and root rot of potato plants in fields. Fifty four isolates from potato, bean, chickpea and cucurbit (melon, watermelon and cucumber) was subjected in a study through analysis of vegetative compatibility groups (VCGs) and rep-PCR DNA fingerprinting. Nit mutants were used to force heterokaryon formation to determine VCGs and Twenty three groups were determined which designated as VCG A to VCG W. VCG A, was the largest group with 18 members and VCG B, VCG C and VCG D were composed of 8, 6 and 3, respectively. Other groups were identified as two or single-member VCGs. Presence of high single-member VCGs indicates that there is a high level of genetic diversity among isolates and isolates of each host classify in different VCGs. Dendrogram generated using data of rep-PCR, suggests high level of genetic diversity among the isolates and no correlation between DNA fingerprinting groups and host and geographical origin of the isolates. Pathogenicity of twenty three F. solani isolates as VCGs representatives originated from mentioned hosts was examined on plants and tubers of Agria cultivar of potato. Except four and two isolates, other isolates were pathogenic on potato plants and tubers. Pathogenicity tests distinguished that F. solani isolates do not have host specific behavior and isolates obtained from non-potato hosts are able to cause disease on potato plants and tubers.
Show more [+] Less [-]Genetic diversity and phylogentic analysis of Sweet potato feathery mottle virus and sweet potato virus G in Sichuan, China Full text
2014
Deng, X.G. | Zhu, F. | Li, J.Y. | Feng, H. | Xi, D.H. | Lin, H.H.
The genetic diversity and phylogenetic relationships of Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus G (SPVG), two major sweet potato viruses in Sichuan, the largest sweet potato producing area of China, were analyzed. A total of 18 virus isolates, including 12 SPFMV isolates and six SPVG isolates, were obtained from different fields and characterized by RT-PCR and sequencing. Sequence alignments revealed 77.3%-99.8% and 85.4%-99.6% nucleotide identities for the coat protein gene of SPFMV and SPVG, respectively. Phylogenetic analysis divided SPFMV isolates into groups RC, O and C, and SPGV isolates into groups CH and CH2. The information presented in this study is useful for the development of engineered resistance to local virus strains in sweet potato.
Show more [+] Less [-]Ruta Condor (Route of the Condor) Full text
2014
julian gonsalves
The project aimed at restoring and conserving the genetic diversity of native potatoes in situ �?? high in the Andes, where the crops originated. Scientists, farmers, and local partners repatriated over 4,600 samples of more than 1,200 varieties of native potato in 41 locations, following the ancient north south pre-Columbian route that unified the Inca Empire. Cultivation of various varieties by numerous families is done using the 'potato park' model | Julian Gonsalves, 'Ruta Condor (Route of the Condor)', CCAFS, 2014
Show more [+] Less [-]Representing SSR molecular marker profiles using concepts from Andean khipus Full text
2014
Simon, R. | Carhuapoma, Pablo | Hualla, V. | Ghislain, M. | Mendiburu, F. de | Gómez, R. | Zorrilla, C. | Roca, W. | Haan, Stef de | Bonierbale, Merideth W.
Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. The International Potato Center presently uses a SSR marker-kit to create molecular profiles for potato accessions. We identified a need for a compact graphical representation that allows comparative presentation of molecular diversity and accession characteristics - thereby permitting biologists and collection curators to have a simple means to interpret molecular data. Inspired by the ancient Andean qipus we devised a graph that standardizes representation while leaving room for updates of the marker kit and the collection of accessions. The molecular khipu permits combining and annotating a set of SSR loci with allele frequency and allele size distribution information. The design is flexible to incorporate updates on genetic diversity information. Graphical means facilitate reading of allele diversity information. As a compact graphical view it facilitates information storage and exchange. The SSR khipu will be useful to other genebanks and breeders. Software to create graphics in single or batch mode is available as R package ’khipu’.
Show more [+] Less [-]Genetic diversity analysis of a potato (Solanum tuberosum L.) collection including Chiloé Island landraces and a large panel of worldwide cultivars Full text
2014
Esnault, F. | Solano, J. | Perretant, M. R. | Hervé, M. | Label, A. | Pellé, R. | Dantec, J. P. | Boutet, G. | Brabant, P. | Chauvin, J. E.
Genetic diversity analysis of a potato (Solanum tuberosum L.) collection including Chiloé Island landraces and a large panel of worldwide cultivars Full text
2014
Esnault, F. | Solano, J. | Perretant, M. R. | Hervé, M. | Label, A. | Pellé, R. | Dantec, J. P. | Boutet, G. | Brabant, P. | Chauvin, J. E.
In order to investigate further the interest of using the Chilean gene pool in potato breeding programmes, the genetic diversity and population structure of a collection of Solanum tuberosum L. genotypes including 350 worldwide varieties or breeders' lines (referred to as the modern group) and 30 Chiloé Island landraces were examined using simple sequence repeat markers. The close genetic proximity of the Chiloé Island landraces to the modern group was confirmed using several structure analysis methods: principal coordinate analysis; hierarchical clustering analysis; analysis of molecular variance; Bayesian model-based clustering analysis. The latter analysis, in particular, revealed no clear genetic structure between the modern group and the Chiloé Island landraces. The Chiloé Island germplasm appears to represent an interesting gene pool that could be exploited in potato breeding programmes using an association mapping approach.
Show more [+] Less [-]Genetic diversity analysis of a potato (Solanum tuberosum L.) collection including Chiloé Island landraces and a large panel of worldwide cultivars Full text
2014
Esnault, Florence | Solano, J. | Perretant, Marie-Reine | Herve, Marie | Label-Richardson, Alain | Pellé, Roland | Dantec, Jean-Paul | Boutet, Gilles | Brabant, Philippe | Chauvin, Jean-Eric | Institut de Génétique, Environnement et Protection des Plantes (IGEPP) ; Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST | Catholic University of Temuco | Génétique Diversité et Ecophysiologie des Céréales (GDEC) ; Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP) | Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon) ; Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)
International audience | In order to investigate further the interest of using the Chilean gene pool in potato breeding programmes, the genetic diversity and population structure of a collection of Solanum tuberosum L. genotypes including 350 worldwide varieties or breeders' lines (referred to as the modern group) and 30 Chiloé Island landraces were examined using simple sequence repeat markers. The close genetic proximity of the Chiloé Island landraces to the modern group was confirmed using several structure analysis methods: principal coordinate analysis; hierarchical clustering analysis; analysis of molecular variance; Bayesian model-based clustering analysis. The latter analysis, in particular, revealed no clear genetic structure between the modern group and the Chiloé Island landraces. The Chiloé Island germplasm appears to represent an interesting gene pool that could be exploited in potato breeding programmes using an association mapping approach.
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