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Chen J, Tao F, Xue Y, Xu B, Li X. Genome-Wide Identification of the WRKY Gene Family and Functional Characterization of CpWRKY5 in Cucurbita pepo. Int J Mol Sci 2024; 25:4177. [PMID: 38673762 PMCID: PMC11049939 DOI: 10.3390/ijms25084177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/27/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I-III), with Group II further divided into five subgroups (IIa-IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.
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Affiliation(s)
- Junhong Chen
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Fei Tao
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingyu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaowei Li
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
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Gavilan NH, de Freitas Morel LJ, da Silva Coppede J, Taleb-Contini SH, de Castro França S, Bertoni BW, Pereira AMS. Genetic diversity and verbascoside content in natural populations of Pyrostegia venusta (Ker Gawl.) Miers. Mol Biol Rep 2022; 49:8617-8625. [PMID: 35867291 DOI: 10.1007/s11033-022-07697-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Pyrostegia venusta (Ker Gawl.) Miers occurs in threatened biodiversity hotspots of Cerrado and Atlantic forest biomes in Brazil and is used in traditional medicine to treat various respiratory and skin diseases. METHODS AND RESULTS This study (i) examined the genetic diversity and structure of six natural populations of P. venusta from different Brazilian regions using sequence-related amplified polymorphism (SRAP) markers; and (ii) compared the intra- and inter-populational levels of the bioactive component verbascoside using high-performance liquid chromatography. The population from Nova Mutum, Mato Grosso, presented the highest genetic variability (Nei index H = 0.2759; Shannon index I = 0.4170; 85.14% polymorphic loci), whereas the population from Araxá, Minas Gerais, presented the lowest genetic variability (H = 0.1811; I = 0.2820; 70.27% polymorphic loci). The intra-populational variability (79%) was significantly higher (p = 0.001) than the inter-populational variability (21%). The populations were clustered into two groups but their genetic differentiation was not associated with geographical origin (Mantel test, r = 0.328; p > 0.05). The verbascoside content significantly differed (p > 0.05) among the six populations and between the individuals from each population. The highest verbascoside levels (> 200 µg/mg extract) were detected in populations from Araxá and Serrana, while the lowest verbacoside levels were detected in populations from Paranaíta and Sinop. CONCLUSIONS This is the first report on the use of SRAP markers to analyze genetic variability in the family Bignoniaceae. Our findings shall help to better understand the genetic and chemical diversity of P. venusta populations, as well as provide useful information to select the most appropriate individuals to prepare phytomedicines.
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Affiliation(s)
- Natália Helena Gavilan
- Departamento de Horticultura, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, São Paulo, 18618-970, Brazil
| | - Lucas Junqueira de Freitas Morel
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Juliana da Silva Coppede
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Silvia Helena Taleb-Contini
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Suzelei de Castro França
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Bianca Waléria Bertoni
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil.,Jardim Botânico de Plantas Medicinais Ordem e Progresso, Jardinópolis, São Paulo, 14680-000, Brazil
| | - Ana Maria Soares Pereira
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil. .,Jardim Botânico de Plantas Medicinais Ordem e Progresso, Jardinópolis, São Paulo, 14680-000, Brazil.
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Lira-Ortiz R, Cortés-Cruz MA, López-Guzmán GG, Palomino-Hermosillo YA, Sandoval-Padilla I, Ochoa-Jiménez VA, Sánchez-Herrera LM, Balois-Morales R, Berumen-Varela G. Diversidad Génetica de poblaciones de guanábana (Annona muricata L.) en Nayarit, México mediante marcadores SSR y SRAP. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v27n1.88241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La guanábana (Annona muricata) es un cultivo de importancia económica para Nayarit, México. Los frutos han tenido una excelente aceptación en el mercado regional, dificultando su comercialización a lugares lejanos porque la producción es altamente perecedera, aunado a que los árboles de los huertos de guanábana son en su mayoría ecotipos o fenotipos sin ningún plan de mejoramiento genético. Debido a la falta de variedades comerciales y de un banco de germoplasma, es importante conocer la diversidad genética para identificar y seleccionar genotipos; una de las herramientas para este propósito es el uso de marcadores moleculares. El objetivo de esta investigación fue analizar la diversidad genética de guanábana de las principales zonas productoras de Nayarit. Se extrajo ADN genómico de hojas de guanábana, las cuales fueron recolectadas de 11 huertos (poblaciones) de las siguientes zonas: Compostela (cinco poblaciones), Tepic (tres poblaciones) y San Blas (tres poblaciones). Posteriormente, se realizó un análisis mediante marcadores moleculares SSR y SRAP. Los resultados indicaron que los SSR no mostraron polimorfismo entre las poblaciones. Por otro lado, en los marcadores SRAP se obtuvieron 116 loci polimórficos con un promedio de porcentaje de loci polimórfico (P) entre las zonas productoras de 29,55 %. Asimismo, se realizó un AMOVA, el cual mostró que el mayor porcentaje de varianza se encuentra dentro de las poblaciones. Además, los análisis de agrupamiento demostraron la formación de tres grupos independientes. Por tanto, se obtuvo una alta homocigocidad y baja diversidad genética de guanábana entre las zonas y poblaciones estudiadas.
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Yarar G, Kocak M, Denli N, Cavagnaro PF, Yildiz M. Determination of the effective radiation dose for mutation breeding in purple carrot (Daucus carota L.) and possible variations formed. Mol Biol Rep 2021; 49:5219-5228. [PMID: 34363560 DOI: 10.1007/s11033-021-06618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/02/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Plant breeding allows altering the genetic structure of plants to meet human needs. The use of radiation technology for inducing mutations and -thereby- new phenotypic variants has become increasingly common as a tool for developing new crops. The aim of this study was to determine the effective gamma irradiation dose for inducing mutations in purple carrot. METHODS AND RESULTS Increasing gamma radiation doses [0, 50, 100, 200, 300, 400, 500, and 600 Gy] were applied to purple carrot seeds. The irradiated seeds were sown in pots and the emergence and survival rates of the seedlings were analyzed. Considering plant emergence (%) as a response variable, the LD50 dose was 387.5 Gy. Analysis of root length, root width (shoulder diameter) and plant height in control (0 Gy) and irradiated plants (50-600 Gy) revealed an inverse association between these morphological traits and radiation dose. SRAP and ISSR markers were used to identify DNA polymorphisms in irradiated and control plants. The range of amplicons per primer set revealed by ISSR and SRAP markers was 4-10 and 2-13, respectively. In the ISSR analysis of the irradiated carrots (for the 8 doses used), we obtained range values for the average Nei's gene diversity, Shannon's information index, and polymorphism information content (PIC) of 0.13-0.25, 0.20-0.35, and 1.39-1.67, respectively, whereas in the SRAP analysis, the range values for these parameters were 0.15-0.25, 0.23-0.37, and 0.43-0.58, respectively. Cluster analysis revealed three main groups; (a) non-irradiated (control) plants, (b) plants from the 600 Gy dose, and (c) a third group with two subgroups: one with individuals from the lowest irradiation doses (50-200 Gy) and a second group with individuals from the highest irradiation doses (300-500 Gy). CONCLUSIONS This is the first report on determining effective mutagen doses and genetic characterization of induced mutagenesis via gamma irradiation in purple carrot. ISSR and SRAP markers were successful in detecting variations among different levels of mutagen doses.
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Affiliation(s)
- Gülistan Yarar
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Metin Kocak
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Nihal Denli
- Alata Horticultural Research Institute, Mersin, Turkey
| | - Pablo F Cavagnaro
- National Council of Scientific and Technical Research (CONICET), and National Institute of Agricultural Technology (INTA) E.E.A. La Consulta, Mendoza, Argentina
| | - Mehtap Yildiz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080, Van, Turkey.
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Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7060143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.
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Martínez-González C, Castellanos-Morales G, Barrera-Redondo J, Sánchez-de la Vega G, Hernández-Rosales HS, Gasca-Pineda J, Aguirre-Planter E, Moreno-Letelier A, Escalante AE, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.656051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.
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7
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Nyadanu D, Lowor ST, Akpertey A, Tchokponhoué DA, Pobee P, Dogbatse JA, Okyere D, Amon-Armah F, Brako-Marfo M. Genetic variability of bioactive compounds and selection for nutraceutical quality in kola [Cola nitida (Vent) Schott. and Endl.]. PLoS One 2020; 15:e0242972. [PMID: 33270707 PMCID: PMC7714174 DOI: 10.1371/journal.pone.0242972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
Cola nitida known as Kola serves as flavouring ingredient in the food industry and is also of great importance during traditional rites in Africa. Despite the well-known pharmaceutical values of the species, efforts to develop improved varieties with enhanced nutraceutical quality is limited due to unavailability of information on variation of genotypes in bioactive compounds in the nuts. The objectives of this research were to evaluate 25 genotypes of kola for bioactive contents, determine relationship between nutritional and phenolic traits and to identify kola genotypes with good nutraceutical quality for use in developing improved varieties. The kola genotypes were established in the field using a randomized complete block design with three replicates. Nuts harvested from the blocks, were bulked and used to quantify soluble and insoluble sugars, total protein, moisture, ash, fats, pH, polyphenols, tannins and flavonoids using completely randomized design with three replicates in the laboratory. Data were analysed by combining Analysis of Variance, Kruskal-Wallis test, correlation test and multivariate analysis. Significant variations (P < 0.05) were observed among the kola genotypes for the bioactive traits evaluated. Phenolic traits were more heritable than nutritional traits. Although not significant (P > 0.05), correlation between nutritional and phenolic traits was negative, whereas correlations among nutritional traits were weak. On the contrary, significant and positive correlations (P < 0.05) were observed among phenolic traits. The hierarchical clustering analysis based on the traits evaluated grouped the 25 genotypes of kola evaluated into four clusters. Genotypes A12, JB4, JB19, JB36, P2-1b, and P2-1c were identified as potential parental lines for phenolic traits selection in kola whereas genotypes A10, Club, Atta1 and JB10 can be considered for soluble and insoluble sugar-rich variety development. These findings represent an important step towards improving nutritional and nutraceutical quality of kola nuts.
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Affiliation(s)
| | | | | | - Dèdéou Apocalypse Tchokponhoué
- Faculty of Agronomic Sciences, Laboratory of Genetics, Biotechnology and Seed Science, University of Abomey-Calvi, Abomey-Calavi, Republic of Benin
| | - Prince Pobee
- Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | | | - Daniel Okyere
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Genetic diversity analysis of Corynespora cassiicola isolates on the rubber tree (Hevea brasiliensis) in Vietnam using ribosomal DNA internal transcribed spacer (rDNA-ITS) sequences and sequence-related amplified polymorphism (SRAP). J RUBBER RES 2020. [DOI: 10.1007/s42464-020-00047-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Ye H, Wu J, Wang Z, Hou H, Gao Y, Han W, Ru W, Sun G, Wang Y. Population genetic variation characterization of the boreal tree Acer ginnala in Northern China. Sci Rep 2020; 10:13515. [PMID: 32782277 PMCID: PMC7419535 DOI: 10.1038/s41598-020-70444-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.,Changzhi University, Changzhi, 046011, Shanxi, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wenming Ru
- Changzhi University, Changzhi, 046011, Shanxi, China.
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, B3H3C3, Canada.
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.
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Nguyen NN, Kim M, Jung JK, Shim EJ, Chung SM, Park Y, Lee GP, Sim SC. Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin ( Cucurbita spp.). HORTICULTURE RESEARCH 2020; 7:121. [PMID: 32821404 PMCID: PMC7395168 DOI: 10.1038/s41438-020-00342-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 05/24/2023]
Abstract
Three pumpkin species Cucurbita maxima, C. moschata, and C. pepo are commonly cultivated worldwide. To identify genome-wide SNPs in these cultivated pumpkin species, we collected 48 F1 cultivars consisting of 40 intraspecific hybrids (15 C. maxima, 18 C. moschata, and 7 C. pepo) and 8 interspecific hybrids (C. maxima x C. moschata). Genotyping by sequencing identified a total of 37,869 confident SNPs in this collection. These SNPs were filtered to generate a subset of 400 SNPs based on polymorphism and genome distribution. Of the 400 SNPs, 288 were used to genotype an additional 188 accessions (94 F1 cultivars, 50 breeding lines, and 44 landraces) with a SNP array-based platform. Reliable polymorphisms were observed in 224 SNPs (78.0%) and were used to assess genetic variations between and within the four predefined populations in 223 cultivated pumpkin accessions. Both principal component analysis and UPGMA clustering found four major clusters representing three pumpkin species and interspecific hybrids. This genetic differentiation was supported by pairwise Fst and Nei's genetic distance. The interspecific hybrids showed a higher level of genetic diversity relative to the other three populations. Of the 224 SNPs, five subsets of 192, 96, 48, 24, and 12 markers were evaluated for variety identification. The 192, 96, and 48 marker sets identified 204 (91.5%), 190 (85.2%), and 141 (63.2%) of the 223 accessions, respectively, while other subsets showed <25% of variety identification rates. These SNP markers provide a molecular tool with many applications for genetics and breeding in cultivated pumpkin.
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Affiliation(s)
- Nam Ngoc Nguyen
- Department of Bioresources Engineering, Sejong University, Seoul, 05006 South Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul, 05006 South Korea
| | - Jin-Kee Jung
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon, 39660 South Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon, 39660 South Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul, 04620 South Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang, 50463 South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung, 17546 South Korea
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul, 05006 South Korea
- Plant Engineering Research Institute, Sejong University, Seoul, 05006 South Korea
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11
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Differential Gene Expression Responding to Low Phosphate Stress in Leaves and Roots of Maize by cDNA-SRAP. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8420151. [PMID: 32775444 PMCID: PMC7391117 DOI: 10.1155/2020/8420151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022]
Abstract
Phosphate (Pi) deficiency in soil can have severe impacts on the growth, development, and production of maize worldwide. In this study, a cDNA-sequence-related amplified polymorphism (cDNA-SRAP) transcript profiling technique was used to evaluate the gene expression in leaves and roots of maize under Pi stress for seven days. A total of 2494 differentially expressed fragments (DEFs) were identified in response to Pi starvation with 1202 and 1292 DEFs in leaves and roots, respectively, using a total of 60 primer pairs in the cDNA-SRAP analysis. These DEFs were categorized into 13 differential gene expression patterns. Results of sequencing and functional analysis showed that 63 DEFs (33 in leaves and 30 in roots) were annotated to a total of 54 genes involved in diverse groups of biological pathways, including metabolism, photosynthesis, signal transduction, transcription, transport, cellular processes, genetic information, and organismal system. This study demonstrated that (1) the cDNA-SRAP transcriptomic profiling technique is a powerful method to analyze differential gene expression in maize showing advantageous features among several transcriptomic methods; (2) maize undergoes a complex adaptive process in response to low Pi stress; and (3) a total of seven differentially expressed genes were identified in response to low Pi stress in leaves or roots of maize and could be used in the genetic modification of maize.
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Zhao X, Zou G, Zhao J, Hu L, Lan Y, He J. Genetic relationships and diversity among populations of Paris polyphylla assessed using SCoT and SRAP markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1281-1293. [PMID: 32549689 PMCID: PMC7266889 DOI: 10.1007/s12298-020-00808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/07/2020] [Accepted: 03/27/2020] [Indexed: 05/22/2023]
Abstract
The genetic diversity of 33 Paris polyphylla samples collected from the Dabie Mountains was analyzed using SCoT and SRAP molecular markers, revealing the genetic relationships among Paris polyphylla resources in the Dabie Mountains at the molecular level and providing a theoretical basis for genetic improvement and conservation. As a result, a total of 134 bands were amplified with 9 SCoT primers, the percentage of polymorphic bands was 100%, the average number of primers amplified was 14.89, the PIC value was 94.83% and the genetic similarity coefficient ranged from 0.463 to 0.896. Ten pairs of SRAP primer combinations amplified 135 bands, including 129 polymorphic bands, and the percentage of polymorphic bands was 95.56%. The average number of polymorphic bands obtained with each pair of SRAP primer combinations was 12.9, the PIC value was 93.91%, and the genetic similarity coefficient ranged from 0.533 to 0.904. This study showed that both SCoT and SRAP markers were suitable for the genetic diversity analysis of P. polyphylla, which belongs to a genus in which SRAP marker technology has not previously been applied, despite its application in a variety of other plants.
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Affiliation(s)
- Xiaopei Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Gaofen Zou
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jie Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Linyi Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Yuefeng Lan
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jinling He
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
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Li J, Qi C, Gu J, Jin Z. Effect of sire population on the genetic diversity and fitness of F1 progeny in the endangered Chinese endemic Sinocalycanthus chinensis. Ecol Evol 2020; 10:4091-4103. [PMID: 32489633 PMCID: PMC7244809 DOI: 10.1002/ece3.6179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 11/23/2022] Open
Abstract
Sinocalycanthus chinensis Cheng et S. Y. Chang (Calycanthaceae), which has a unique systematic status, is listed as a national second-class protected plant of China. In this study, the genetic diversity, performance, and fitness of F1 progeny from crosses between the Damingshan (DMS) population of S. chinensis and pollen parents from the Daleishan (DLS) and Longxushan (LXS) populations were examined. The DLS population has a relatively small population size, low genetic diversity, and considerable geographical and genetic distances from the DMS population relative to the LXS population. Compared with naturally occurring seeds, DLS-sired seeds had the highest thousand-seed weight, starch content, fat content, germination rate, germination index, and emergence rate, but the lowest protein content. Naturally occurring, open-pollinated seeds had the lowest thousand-seed weight, starch content, and fat content, but the highest protein content. Compared with natural F1 progeny, DMS × DLS seedlings had the highest genetic diversity, photosynthetic parameters, and growth characteristics, except for leaf mass ratio and stem mass ratio. Under strong light, DMS × DLS seedlings exhibited a F v/F m value of 0.75, while the other two seedling types exhibited F v/F m values of 0.65. DLS-sired seeds had the most vigorous growth characteristics except for leaf mass ratio and stem mass ratio. These results suggest that genetic rescue by transplanting seedlings from the DLS population or hand pollination with pollen from the DLS population would be effective methods to reduce inbreeding depression and obtain strong offspring with high genetic diversity and fitness in the DMS population.
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Affiliation(s)
- Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
| | - Caihong Qi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Traffic Patrol Headquarters of Public Security Bureau of Chongqing CityVehicle Management InstituteChongqinChina
| | - Jingjing Gu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
- Xianju Branch of Ecological Environment Bureau of Taizhou CityTaizhouChina
| | - Zexin Jin
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou UniversityTaizhouChina
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Kaźmińska K, Hallmann E, Korzeniewska A, Niemirowicz-Szczytt K, Bartoszewski G. Identification of Fruit-Associated QTLs in Winter Squash ( Cucurbita maxima Duchesne) Using Recombinant Inbred Lines. Genes (Basel) 2020; 11:genes11040419. [PMID: 32295204 PMCID: PMC7230694 DOI: 10.3390/genes11040419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 01/18/2023] Open
Abstract
Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.
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Affiliation(s)
- Karolina Kaźmińska
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Ewelina Hallmann
- Department of Functional and Organic Food, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Aleksandra Korzeniewska
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
- Correspondence:
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Hernández-Rosales HS, Castellanos-Morales G, Sánchez-de la Vega G, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient. AMERICAN JOURNAL OF BOTANY 2020; 107:510-525. [PMID: 32072632 DOI: 10.1002/ajb2.1424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. METHODS We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. RESULTS Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans-Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well-differentiated group. CONCLUSIONS Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.
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Affiliation(s)
- Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Villahermosa, Carretera Villahermosa-Reforma km 15.5 Ranchería El Guineo 2ª sección, 86280, Villahermosa, Tabasco, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías, Km 6.5 carretera Celaya-San Miguel de Allende, C.P. 38110, Celaya, Guanajuato, México, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, 54090, Tlanepantla, Edo. de Mex, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
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16
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Xiong M, Wang Y, Chen D, Wang X, Zhou D, Wei Z. Assessment of genetic diversity and identification of core germplasm in single-flowered amaryllis ( Hippeastrum hybridum) using SRAP markers. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1814865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Min Xiong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
| | - Yi Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, PR China
| | - Defeng Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
| | - Xian Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
| | - Di Zhou
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
| | - Zunzheng Wei
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing Engineering Technology Research Center of Functional Floriculture, Beijing, PR China
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Castellanos-Morales G, Ruiz-Mondragón KY, Hernández-Rosales HS, Sánchez-de la Vega G, Gámez N, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Tracing back the origin of pumpkins (Cucurbita pepo ssp. pepo L.) in Mexico. Proc Biol Sci 2019; 286:20191440. [PMID: 31409251 PMCID: PMC6710597 DOI: 10.1098/rspb.2019.1440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/23/2019] [Indexed: 11/12/2022] Open
Abstract
Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo's ancestor.
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Affiliation(s)
- Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa, Villahermosa, Tabasco, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Karen Y. Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Helena S. Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Niza Gámez
- Facultad de Estudios Superiores, Zaragoza, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías (INIFAP), Celaya, Guanajuato, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
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Podyma W, Bolc P, Nocen J, Puchta M, Wlodarczyk S, Lapinski B, Boczkowska M. A multilevel exploration of Avena strigosa diversity as a prelude to promote alternative crop. BMC PLANT BIOLOGY 2019; 19:291. [PMID: 31269919 PMCID: PMC6610812 DOI: 10.1186/s12870-019-1819-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Sand oat (Avena strigosa Schreb.), one of the four cultivated species of the genus Avena, could be considered as another alternative crop. In gene banks 865 germplasm samples of this species have been preserved that have not been thoroughly investigated so far. The results of phenotyping (36 traits), isoenzymatic (12 systems) and genetic (8 pairs of Sequence-related amplified polymorphism markers) variation were used to obtain the complete description of 56 accessions diversity originated from different parts of world. RESULTS Breeded and weedy forms represented similar pool of morphological traits that indicated a short-term and extensive breeding process, albeit all accessions which we classified as cultivated were characterized by better grain and green mass parameters compared to the weedy ones. Isoenzymes showed relationships with geographical origin, which was not possible to detect by SRAP markers. There was no similarity between morphological and biochemical results. The polymorphism level of SRAP markers was lower than indicated by the available literature data for other species, however it may result from the analysis of pooled samples of accessions with a high internal variability. The extensive type of breeding and its relatively short duration was also reflected in the population structure results. Joint analysis revealed that a secondary centre of diversity is being created in South America and that it has its genealogy from the Iberian Peninsula. CONCLUSIONS Despite the relatively large representation of this species is in various gene banks, it is highly probable that the vast majority of stored worldwide accessions are duplicates, and the protected gene pool is relatively narrow. Sand oat meets all the requirements for an alternative crop species, but further studies are needed to identify the genotypes/populations with the most favourable distribution of utility and quality parameters.
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Affiliation(s)
- Wiesław Podyma
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
| | - Paulina Bolc
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Joanna Nocen
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Marta Puchta
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Sylwia Wlodarczyk
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Boguslaw Lapinski
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Maja Boczkowska
- Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland.
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warszawa, Poland.
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Youssef AF, Younes NA, Youssef M. Genetic diversity in Corchorus olitorius L. revealed by morphophysiological and molecular analyses. Mol Biol Rep 2019; 46:2933-2940. [PMID: 30887258 DOI: 10.1007/s11033-019-04754-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/08/2019] [Indexed: 12/01/2022]
Abstract
Assessment of genetic diversity has an efficient role in plant breeding and improvement programs. There is a limit number of investigations dealing with the evaluation of genetic diversity in Jew's mallow (Corchorus olitorius L.), despite its valuable importance as a leafy vegetable and a delicious dish rich in vitamins and antioxidants. Therefore, in this study, 18 landraces of Jew's mallow-collected from different locations in Egypt-were used for genetic diversity assessment based on morphophysiological and molecular evaluations. A high degree of variability was found among the evaluated landraces at both levels, indicating the appropriateness of such collection to be involved in breeding approaches. Some morphophysiological traits offered a high level of diversity and effectively discriminated the landraces. Thus, they are recommended to be used in successive morphological evaluation studies. On the other hand, molecular evaluation using the random amplified polymorphic DNA (RAPD) and the sequence related amplified polymorphism (SRAP) efficiently supported the morphological results by exposing a clear genetic relationship among the landraces. In addition, the principal coordinate analysis based on combined data of RAPD and SRAP divided the landraces into two main groups, reflecting their relationship molecularly. The first group included nine landraces related to Upper Egypt and the second gathered three landraces from Delta, while the other six landraces were distinctly distributed around these two groups. The two groups may have two distinct ancestors in addition to the different ancestors of the scattered landraces. Findings of this study are valuable and could assist in Jew's mallow breeding programs.
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Affiliation(s)
- Ahmed Fathy Youssef
- Department of Horticulture, Faculty of Agriculture, Al-Azhar University-Assiut - Branch, Assiut, Egypt
| | - Nabil Ahmed Younes
- Department of Horticulture, Faculty of Agriculture, Al-Azhar University-Assiut - Branch, Assiut, Egypt
| | - Muhammad Youssef
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
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20
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Huang L, Yan X. Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades. PLoS One 2019; 14:e0209128. [PMID: 30849086 PMCID: PMC6407771 DOI: 10.1371/journal.pone.0209128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/20/2019] [Indexed: 11/18/2022] Open
Abstract
Pyropia yezoensis is an economically important seaweed but its molecular genetics is poorly understood. In the present study, we used a doubled haploid (DH) population that was established in our previous work to construct a genetic linkage map of P. yezoensis and analyze the quantitative trait loci (QTLs) of blades. The DH population was genotyped with fluorescent sequence-related amplified polymorphism (SRAP) markers. A chi-square test identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The genetic map was constructed after a total of 92 loci were assembled into three linkage groups (LGs). The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α = 5%) showed a uniform distribution of the markers along each LG. On the genetic map, 10 QTLs associated with five economic traits of blades were detected. One QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29–7.87% of the trait variations, indicating that their effects were all minor. The results may serve as a framework for future marker-assisted breeding in P. yezoensis.
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Affiliation(s)
- Linbin Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
| | - Xinghong Yan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
- * E-mail:
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21
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Intra-population genetic diversity of Buchloe dactyloides (Nutt.) Engelm (buffalograss) determined using morphological traits and sequence-related amplified polymorphism markers. 3 Biotech 2019; 9:97. [PMID: 30800608 DOI: 10.1007/s13205-019-1632-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/11/2019] [Indexed: 10/27/2022] Open
Abstract
Genetic variation and diversity are prerequisites for improvement of buffalograss breeding. To assess the within-population genetic diversity of buffalograss, seven morphological traits were evaluated to confirm the variations at the morphological level. The principal component analysis revealed that leaf length, leaf width and stolon branches had a significant contribution to the total variation. The first three principle components showed 72.55% variation. The DNA analysis performed using SRAP primers was used for deducing the diversity at the DNA level. A total of 125 bands were obtained with 8 selected SRAP primer pairs, of which 119 (95.2%) were polymorphic. The polymorphic information content ranged from 0.94 to 0.97 with a mean of 0.96; the marker index ranged from 10.34 to 18.43 with an average value of 14.28. The individuals were successfully assigned to two major groups according to sex in the PCoA and UPGMA dendrogram based on SRAP data, while the individuals could not be grouped based on morphological traits, and the two markers were not significantly correlated (r = 0.0753, P = 0.8489 > 0.05). The molecular data revealed that sex is a critical factor and that female and monoecious plants could be chosen as parents to breed new varieties.
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Akbar A, Hussain S, Ullah K, Fahim M, Ali GS. Detection, virulence and genetic diversity of Fusarium species infecting tomato in Northern Pakistan. PLoS One 2018; 13:e0203613. [PMID: 30235252 PMCID: PMC6147440 DOI: 10.1371/journal.pone.0203613] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
In addition to the well-known Fusarium oxysporum f.sp. lycopersici, several other Fusarium species are known to cause extensive worldwide crop losses in tomatoes. Prevalence and identities of Fusarium species infecting tomatoes in Northwest Pakistan is currently not known. In this study, we surveyed and characterized Fusarium species associated with symptomatic tomatoes in Northwest Pakistan using morphological and molecular analyses. Pathogenicity tests revealed varying degrees of virulence with some Fusarium sp. causing severe disease symptoms whereas others displaying mild symptoms. Molecular identification based on Internal Transcribed Spacer (ITS) region and TEF-1α gene sequencing classified all isolates into four major species with a majority (68.9%) belonging to Fusarium incarnatum-equiseti species complex (FIESC), followed by F. graminearum (20.7%), F. acuminatum (6.8%), and F. solani (6.8%). ISSR analyses revealed substantial genetic variability among all the Fusarium population infecting tomatoes. Genetic distance between populations from the central region and the type strain F.o. f.sp. lycopersici from Florida was the highest (0.3662), whereas between the south and central region was the lowest (0.0298), which showed that genetic exchange is negatively effected by distance. High genetic variability suggests that these Fusarium species have the potential to become a major production constraint for tomato growers. Findings in this report would greatly facilitate identification of Fusarium species in developing countries and would provide groundwork for devising and implementing disease management measures for minimizing losses caused by Fusarium species in tomatoes.
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Affiliation(s)
- Asma Akbar
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, Institute of Food and Agricultural Sciences, Apopka, FL, United States of America
| | - Shaukat Hussain
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Kaleem Ullah
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Muhammad Fahim
- Khyber-Pakhtumkhwa Agriculture University, Peshawar, Pakistan
| | - Gul Shad Ali
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, Institute of Food and Agricultural Sciences, Apopka, FL, United States of America
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Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: A robust classification approach. Anal Biochem 2018; 550:8-14. [PMID: 29649471 DOI: 10.1016/j.ab.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/08/2018] [Indexed: 11/20/2022]
Abstract
In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies. The utility of the proposed approach is successfully demonstrated by analysing the two different kind of bacterial collections. The first set comprised of peptidoglycan sample belonging to different subclasses of Alphaproteobacteria. Whereas, the second set that is relatively more intricate for the chemometric analysis consist of different wild type Vibrio Cholerae and its mutants having subtle differences in their peptidoglycan composition. The present work clearly proposes a useful approach that can classify the chromatographic data sets of chromatographic peptidoglycan samples having subtle differences. Furthermore, present work clearly suggest that PCoA can be a method of choice in any data analysis workflow.
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Polat İ, Baysal Ö, Mercati F, Gümrükcü E, Sülü G, Kitapcı A, Araniti F, Carimi F. Characterization of Botrytis cinerea isolates collected on pepper in Southern Turkey by using molecular markers, fungicide resistance genes and virulence assay. INFECTION GENETICS AND EVOLUTION 2018; 60:151-159. [PMID: 29505818 DOI: 10.1016/j.meegid.2018.02.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/30/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022]
Abstract
Botrytis cinerea is a polyphagous fungal pathogen causing gray mold disease. Moreover, it is one of the most destructive infections of small fruit crops such as pepper (Capsicum annnum L.). C. sativum is a species belonging to the Solanaceae family and Turkey is one of the main producers in the World. In the present work, aiming to obtain information useful for pest management, fifty B. cinerea isolates collected from Turkey and a reference isolate (B05.10) were characterized using molecular markers and fungicide resistance genes. Morphological and molecular (ITS1-ITS4) identification of B. cinerea isolates, the degree of virulence and mating types were determined. Since one or several allelic mutations in the histidine kinase (Bos1) and β-tubulin genes generally confer the resistance to fungicides, the sequences of these target genes were investigated in the selected isolates, which allowed the identification of two different haplotypes. Mating types were also determined by PCR assays using primer specific for MAT1-1 alpha gene (MAT1-1-1) and MAT1-2 HMG (MAT1-2-1) of B. cinerea. Twenty-two out of 50 isolates (44%) were MAT1-2, while 38% were MAT1-1. Interestingly, out of whole studied samples, 9 isolates (18%) were heterokaryotic or mixed colonies. In addition, cluster and population structure analyses identified five main groups and two genetic pools, respectively, underlining a good level of variability in the analysed panel. The results highlighted the presence of remarkable genetic diversity in B. cinerea isolates collected in a crucial economical area for pepper cultivation in Turkey and the data will be beneficial in view of future gray mold disease management.
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Affiliation(s)
- İlknur Polat
- Batı Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - Ömür Baysal
- Muğla Sıtkı Koçman University, Faculty of Science, Department of Molecular Biology and Genetics, 48000 Muğla, Turkey.
| | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Palermo, Italy
| | - Emine Gümrükcü
- Batı Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - Görkem Sülü
- Batı Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - Aytül Kitapcı
- Batı Akdeniz Agricultural Research Institute, Antalya, Turkey
| | - Fabrizio Araniti
- Mediterranean University of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Carimi
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Palermo, Italy
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Montero-Pau J, Blanca J, Esteras C, Martínez-Pérez EM, Gómez P, Monforte AJ, Cañizares J, Picó B. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing. BMC Genomics 2017; 18:94. [PMID: 28100189 PMCID: PMC5241963 DOI: 10.1186/s12864-016-3439-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
Background Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5–62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified. Conclusions Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the genetic basis of the studied processes in squash. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3439-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Montero-Pau
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Eva Ma Martínez-Pérez
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Pedro Gómez
- Instituto de Investigación y Formación Agraria y Pesquera (IFAPA). Área de Mejora y Biotecnología de cultivos. Camino San Nicolás 1, 04745, La Mojonera, Almería, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Joaquín Cañizares
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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26
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Lees CJ, Li G, Duncan RW. Characterization of Brassica napus L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:155. [PMID: 27942247 PMCID: PMC5104778 DOI: 10.1007/s11032-016-0576-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/20/2016] [Indexed: 06/06/2023]
Abstract
Identifying parental combinations that exhibit high heterosis is a constant target for commercial Brassica napus L. hybrid development programs. Finding high heterotic parental combinations can require hundreds of test crosses and years of yield evaluation. Heterotic pool development could be used to divide breeding material into specific breeding pools and focus the number of parental combinations created. Here, we report the genotypic characterization of 79 B. napus genotypes by calculating genetic distance based on sequence-related amplified polymorphism (SRAP) and genotyping by sequencing (GBS) in association with a neighbour-joining clustering algorithm. Despite the different genotypic analyses, neighbour-joining cluster analysis based on genetic distance of SRAP and GBS produced similar clusters. Homology between SRAP and GBS clusters was approximately 77 % when manually comparing clusters and 68 % when comparing clusters using Compare2Trees. This research demonstrates that SRAP can have similar efficacy when compared to next-generation sequencing technology for heterotic pool classification. This information may provide an important breeding scaffold for the development of hybrid cultivars based upon genetic distance and cluster analysis.
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Affiliation(s)
- Corey J. Lees
- Faculty of Agricultural and Food Sciences, Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Genyi Li
- Faculty of Agricultural and Food Sciences, Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Robert W. Duncan
- Faculty of Agricultural and Food Sciences, Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
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Lust TA, Paris HS. Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan. ANNALS OF BOTANY 2016; 118:53-69. [PMID: 27343231 PMCID: PMC4934399 DOI: 10.1093/aob/mcw080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/17/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Summer squash, the young fruits of Cucurbita pepo, are a common, high-value fruit vegetable. Of the summer squash, the zucchini, C. pepo subsp. pepo Zucchini Group, is by far the most cosmopolitan. The zucchini is easily distinguished from other summer squash by its uniformly cylindrical shape and intense colour. The zucchini is a relatively new cultivar-group of C. pepo, the earliest known evidence for its existence having been a description in a book on horticulture published in Milan in 1901. For this study, Italian-language books on agriculture and cookery dating from the 16th to 19th centuries have been collected and searched in an effort to follow the horticultural development and culinary use of young Cucurbita fruits in Italy. FINDINGS The results indicate that Cucurbita fruits, both young and mature, entered Italian kitchens by the mid-16th century. A half-century later, round and elongate young fruits of C. pepo were addressed as separate cookery items and the latter had largely replaced the centuries-old culinary use of young, elongate bottle gourds, Lagenaria siceraria Allusion to a particular, extant cultivar of the longest fruited C. pepo, the Cocozelle Group, dates to 1811 and derives from the environs of Naples. The Italian diminutive word zucchini arose by the beginning of the 19th century in Tuscany and referred to small, mature, desiccated bottle gourds used as containers to store tobacco. By the 1840s, the Tuscan word zucchini was appropriated to young, primarily elongate fruits of C. pepo The Zucchini Group traces its origins to the environs of Milan, perhaps as early as 1850. The word zucchini and the horticultural product zucchini arose contemporaneously but independently. The results confirm that the Zucchini Group is the youngest of the four cultivar-groups of C. pepo subsp. pepo but it emerged approximately a half-century earlier than previously known.
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Affiliation(s)
- Teresa A Lust
- Dartmouth College, Rassias Center for World Languages and Cultures, 6071 Blunt, Suite 315, Hanover, NH 03755-3526, USA
| | - Harry S Paris
- Agricultural Research Organization, Newe Ya'ar Research Center, PO Box 1021, Ramat Yishay 3009500, Israel
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28
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TRAP and SRAP markers to find genetic variability in complex polyploid Paullinia cupana var. sorbilis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Chen H, He X, Liu Y, Li J, He Q, Zhang C, Wei B, Zhang Y, Wang J. Extraction, purification and anti-fatigue activity of γ-aminobutyric acid from mulberry (Morus alba L.) leaves. Sci Rep 2016; 6:18933. [PMID: 26743028 PMCID: PMC4705516 DOI: 10.1038/srep18933] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/01/2015] [Indexed: 01/11/2023] Open
Abstract
Mulberry (Morus alba L.) is a tree species of Moraceae widely distributed in Southern China. In the present study, the white crystal of γ-aminobutyric acid (GABA) was purified from mulberry leaves, and its bioactivity was also investigated. The main results were as follows: first, the crude GABA was extracted from mulberry leaves by using biochemical methods. Then, the crude was purified by chromatography over an S-8 macroporous resin, Sephadex G-10, and 732 cation exchange resin to yield a white crystal. Lavage administration and exposure of GABA to male NIH mice showed no adverse effects on their growth and development. In an endurance capacity test, the average loaded-swimming time of medium dose was 111.60% longer than the control (P < 0.01). Further investigations showed that relative to that of model control, the respective blood lactate (BL) concentrations of low- and medium-dose were 28.52% and 28.81% lower (P < 0.05), whereas the levels of blood urea nitrogen (BUN) were 36.83% and 40.54% lower (P < 0.05), and that of liver glycogen (LG) levels were 12.81% and 17.22% lower (P < 0.05). The results indicated that GABA has an advantage over taurine of anti-fatigue effect. These findings were indicative of the anti-fatigue activity of GABA.
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Affiliation(s)
- Hengwen Chen
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China.,Postdoctoral Research Station, China Academy of Chinese Medicine Science, Beijing 100700, China
| | - Xuanhui He
- Department of Pharmaceutical Chemistry, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yan Liu
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin 150036, Heilongjiang, China
| | - Jun Li
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
| | - Qingyong He
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
| | - Cuiying Zhang
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
| | - Benjun Wei
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
| | - Ye Zhang
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medicine Science, Beijing 100053, China
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30
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Genetic Resources of Pumpkins and Squash, Cucurbita spp. GENETICS AND GENOMICS OF CUCURBITACEAE 2016. [DOI: 10.1007/7397_2016_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Talebi M, Rahimmalek M, Norouzi M. Genetic diversity of Thymus daenensis subsp. daenensis using SRAP markers. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Physical and chemical characterization in fruit from 22 summer squash (Cucurbita pepo L.) cultivars. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2015.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Zhang X, Chen H, Jiang H, Lu W, Pan J, Qian Q, Xue D. Measuring the damage of heavy metal cadmium in rice seedlings by SRAP analysis combined with physiological and biochemical parameters. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:2292-2298. [PMID: 25359308 DOI: 10.1002/jsfa.6949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/30/2014] [Accepted: 10/04/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Cadmium (Cd) is one of the most poisonous pollutants, and Cd pollution has become the limiting factor of rice production and quality improvement. Therefore it is of significant importance to monitor Cd toxicity by the detection of Cd contamination in rice with biomarkers. In the present study, sequence-related amplified polymorphism (SRAP) and physiological and biochemical methods were applied to determine the toxicological effects of Cd stress on rice. RESULTS With increasing Cd concentration and duration, the content of chlorophyll in the two rice varieties W7 and M63 decreased and that of malondialdehyde increased. This tendency was more apparent in M63. The antioxidant enzymes superoxide dismutase and peroxidase both increased significantly compared with controls. SRAP polymerase chain reaction results indicated significant differences between Cd treatments and controls in terms of SRAP profile, as well as genotypic differences. The genomic template stability (GTS) decreased with increasing Cd concentration and duration. Under the same treatment conditions, the GTS of W7 was higher than that of M63. Comparison analysis revealed that the changes in physiological and biochemical parameters of rice seedlings under Cd stress had a good correlation with the changes in SRAP profile. Furthermore, the changes in SRAP profile showed enhanced sensitivity in the roots of rice seedlings. CONCLUSION The SRAP profile and physiological and biochemical parameters could act as appropriate biomarkers for the measurement of Cd contamination during rice production.
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Affiliation(s)
- Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Huinan Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Hua Jiang
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China
| | - Wenyi Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Jiangjie Pan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qian Qian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
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Yildiz M, Cuevas HE, Sensoy S, Erdinc C, Baloch FS. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Mason AS, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. High-throughput genotyping for species identification and diversity assessment in germplasm collections. Mol Ecol Resour 2015; 15:1091-101. [PMID: 25641370 DOI: 10.1111/1755-0998.12379] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 12/01/2022]
Abstract
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.
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Affiliation(s)
- Annaliese S Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jing Zhang
- Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Reece Tollenaere
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paula Vasquez Teuber
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jessica Dalton-Morgan
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Liyong Hu
- Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guijun Yan
- Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Robert Redden
- Department of Environment and Primary Industries, Australian Grains Genebank, Horsham, VIC, 3401, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.,Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia
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Fan X, Jiang J, Zhang Y, Sun H, Jiao J, Liu C. Genetic diversity assessment of Vitis ficifolia Bge. populations from Henan province of China by SRAP markers. BIOTECHNOL BIOTEC EQ 2015; 29:15-20. [PMID: 26019614 PMCID: PMC4433826 DOI: 10.1080/13102818.2014.984414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/13/2014] [Indexed: 11/01/2022] Open
Abstract
Eighteen sequence-related amplified polymorphism (SRAP) primer combinations were used to assess the genetic diversity of 126 individuals from five different geographical populations of Vitis ficifolia Bge. The numbers of bands scored per primer combination ranged from 8 to 27, with an average of 18.6 bands. At the population level, the percentage of polymorphic bands (PPB), Nei's gene diversity index (H) and Shannon's information index (I) were the highest in the Shihe (Xinyang) population (77.31%, 0.1987, 0.2805) and the lowest in the Linzhou (Anyang) population (55.82%, 0.1112, 0.1727). At the species level, PPB, H and I were 80.56%, 0.2129 and 0.3075, respectively. The genetic differentiation coefficient (GST) was 0.2055 and the gene flow (Nm ) was 1.9328, indicating strong intra-population genetic differentiation. Based on the unweighted pair group method based arithmetic average clustering diagram, the five studied populations may be divided into three groups. The clustering results were almost in accordance with the populations' geographical distribution.
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Affiliation(s)
- Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
| | - Haisheng Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
| | - Jian Jiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences , Zhengzhou , Henan , P.R. China
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Karimi A, Hadian J, Farzaneh M, Khadivi-Khub A. Evaluation of genetic variability, rust resistance and marker-detection in cultivated Artemisia dracunculus from Iran. Gene 2015; 554:224-32. [DOI: 10.1016/j.gene.2014.10.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
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Xu R, Hu D, Chen Z, Zhang P, Jiang X, Tang G. SRAP analysis on genetic relationships of genotypes in the genus Malus Mill. BIOTECHNOL BIOTEC EQ 2014; 28:602-607. [PMID: 26740766 PMCID: PMC4684060 DOI: 10.1080/13102818.2014.948596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/12/2014] [Indexed: 11/22/2022] Open
Abstract
Thirteen sequence-related amplified polymorphism (SRAP) primers combined with polymerase chain reaction (PCR) were used to evaluate the genetic relationships among 24 genotypes of the genus Malus Mill. including Sect. Malus, Baccatus, Sorbomalus and Chloromeles. Out of 115 surveyed fragments, 107 (93.04%) were polymorphic. Coefficients of genetic similarity ranged from 0.538 to 0.868, with an average value of 0.720 between pairs of materials, which indicated the high degree of polymorphism within this species. Cluster analysis showed that all genotypes were divided into six groups. A dendrogram showed that some of the clustered genotypes were largely congruent for geographical distribution. The species in Sect. Malus, Sorbomalus and Chloromeles were separated to a great extent. However, the DNA patterns for some genotype groups did not demonstrate relative agreement in their pedigrees. In Sect. Sorbomalus, M. yunnanesis was independently separated, while M. prattii were clustered in group III with M. bhutanica, M. platycarpa and M. fusca classified into Ser. Kansuenses. Five species originated from the American region were dispersed into two groups within the dendrogram. The conflicts were reflecting their complex genetic backgrounds.
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Affiliation(s)
- Rongxue Xu
- College of Forest Resources and Environment, Nanjing Forestry University , Jiangsu , Nanjing , P. R. China
| | - Dechang Hu
- College of Life Science, Ludong University , Shandong , Yantai , P. R. China
| | - Zhongying Chen
- College of Life Science, Ludong University , Shandong , Yantai , P. R. China
| | - Ping Zhang
- College of Life Science, Ludong University , Shandong , Yantai , P. R. China
| | - Xiaoman Jiang
- College of Life Science, Ludong University , Shandong , Yantai , P. R. China
| | - Gengguo Tang
- College of Forest Resources and Environment, Nanjing Forestry University , Jiangsu , Nanjing , P. R. China
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Huang C, Liu G, Bai C, Wang W. Genetic analysis of 430 Chinese Cynodon dactylon accessions using sequence-related amplified polymorphism markers. Int J Mol Sci 2014; 15:19134-46. [PMID: 25338051 PMCID: PMC4227265 DOI: 10.3390/ijms151019134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 09/10/2014] [Accepted: 10/10/2014] [Indexed: 11/25/2022] Open
Abstract
Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars.
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Affiliation(s)
- Chunqiong Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China.
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China.
| | - Changjun Bai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China.
| | - Wenqiang Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China.
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Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala) revealed by SRAP markers: implications for conservation and management. PLoS One 2014; 9:e108967. [PMID: 25265288 PMCID: PMC4181858 DOI: 10.1371/journal.pone.0108967] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 09/06/2014] [Indexed: 11/19/2022] Open
Abstract
The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism) markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian) and one genetic strain (‘Pujiang No. 1’) of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h) and Shannon's information index (I) values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>‘Pujiang No. 1’>Yuni Lake). Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations), Nanxian and ‘Pujiang No. 1’ (cultured population and genetically selected strain), and Yuni Lake (natural population). Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA), with more genetic divergence existing among populations (55.49%), than within populations (44.51%). This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.
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Guo H, Ding W, Chen J, Chen X, Zheng Y, Wang Z, Liu J. Genetic linkage map construction and QTL mapping of salt tolerance traits in Zoysiagrass (Zoysia japonica). PLoS One 2014; 9:e107249. [PMID: 25203715 PMCID: PMC4159309 DOI: 10.1371/journal.pone.0107249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022] Open
Abstract
Zoysiagrass (Zoysia Willd.) is an important warm season turfgrass that is grown in many parts of the world. Salt tolerance is an important trait in zoysiagrass breeding programs. In this study, a genetic linkage map was constructed using sequence-related amplified polymorphism markers and random amplified polymorphic DNA markers based on an F1 population comprising 120 progeny derived from a cross between Zoysia japonica Z105 (salt-tolerant accession) and Z061 (salt-sensitive accession). The linkage map covered 1211 cM with an average marker distance of 5.0 cM and contained 24 linkage groups with 242 marker loci (217 sequence-related amplified polymorphism markers and 25 random amplified polymorphic DNA markers). Quantitative trait loci affecting the salt tolerance of zoysiagrass were identified using the constructed genetic linkage map. Two significant quantitative trait loci (qLF-1 and qLF-2) for leaf firing percentage were detected; qLF-1 at 36.3 cM on linkage group LG4 with a logarithm of odds value of 3.27, which explained 13.1% of the total variation of leaf firing and qLF-2 at 42.3 cM on LG5 with a logarithm of odds value of 2.88, which explained 29.7% of the total variation of leaf firing. A significant quantitative trait locus (qSCW-1) for reduced percentage of dry shoot clipping weight was detected at 44.1 cM on LG5 with a logarithm of odds value of 4.0, which explained 65.6% of the total variation. This study provides important information for further functional analysis of salt-tolerance genes in zoysiagrass. Molecular markers linked with quantitative trait loci for salt tolerance will be useful in zoysiagrass breeding programs using marker-assisted selection.
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Affiliation(s)
- Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Wanwen Ding
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xuan Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yiqi Zheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Zhiyong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Nie G, Zhang XQ, Huang LK, Xu WZ, Wang JP, Zhang YW, Ma X, Yan YH, Yan HD. Genetic variability and population structure of the potential bioenergy crop Miscanthus sinensis (Poaceae) in Southwest China based on SRAP markers. Molecules 2014; 19:12881-97. [PMID: 25153884 PMCID: PMC6271393 DOI: 10.3390/molecules190812881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 11/16/2022] Open
Abstract
The genus Miscanthus has great potential as a biofuel feedstock because of its high biomass, good burning quality, environmental tolerance, and good adaptability to marginal land. In this study, the genetic diversity and the relationship of 24 different natural Miscanthus sinensis populations collected from Southwestern China were analyzed by using 33 pairs of Sequence Related Amplified Polymorphism (SRAP) primers. A total of 688 bands were detected with 646 polymorphic bands, an average of 19.58 polymorphic bands per primer pair. The average percentage of polymorphic loci (P), gene diversity (H), and Shannon's diversity index (I) among the 24 populations are 70.59%, 0.2589, and 0.3836, respectively. The mean value of total gene diversity (HT) was 0.3373±0.0221, while the allelic diversity within populations (HS) was 0.2589±0.0136 and the allelic diversity among populations (DST) was 0.0784. The mean genetic differentiation coefficient (Gst=0.2326) estimated from the detected 688 loci indicated that there was 76.74% genetic differentiation within the populations, which is consistent with the results from Analysis of Molecular Variance (AMOVA) analysis. Based upon population structure and phylogenetic analysis, five groups were formed and a special population with mixed ancestry was inferred indicating that human-mediated dispersal may have had a significant effect on population structure of M. sinensis. Evaluating the genetic structure and genetic diversity at morphological and molecular levels of the wild M. sinensis in Southwest China is critical to further utilize the wild M. sinensis germplasm in the breeding program. The results in this study will facilitate the biofuel feedstock breeding program and germplasm conservation.
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Affiliation(s)
- Gang Nie
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Xin-Quan Zhang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Lin-Kai Huang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Wen-Zhi Xu
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jian-Ping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.
| | - Yun-Wei Zhang
- Grassland Institute, China Agricultural University, Beijing 100193, China.
| | - Xiao Ma
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Yan-Hong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Hai-Dong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
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Robarts DWH, Wolfe AD. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1400017. [PMID: 25202637 PMCID: PMC4103474 DOI: 10.3732/apps.1400017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/15/2014] [Indexed: 05/10/2023]
Abstract
In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.
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Affiliation(s)
- Daniel W. H. Robarts
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 West 12th Avenue, Columbus, Ohio 43210 USA
| | - Andrea D. Wolfe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 West 12th Avenue, Columbus, Ohio 43210 USA
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Huang CQ, Liu GD, Bai CJ, Wang WQ, Tang J. Application of SRAP markers in the identification of Stylosanthes guianensis hybrids. Mol Biol Rep 2014; 41:5923-9. [PMID: 24965147 DOI: 10.1007/s11033-014-3467-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 06/14/2014] [Indexed: 11/29/2022]
Abstract
Sequence-related amplified polymorphism (SRAP) is a new molecular marker technology developed based on polymerase chain reaction. The authenticity of 84 progenies of 8 hybrid combinations of Stylosanthes guianensis was identified by SRAP markers to select the true hybrids used in the present study. A total of 35 SRAP primer combinations were selected from the parents of 8 hybrid combinations. The selected polymorphism primer combinations were applied to identify the authenticity of all progenies. The male parents of the primer combinations had specific markers, whereas the female parents did not. 68 progenies exhibited male parent-specific bands, which were identified as true hybrids. The rest of the progenies were considered self-hybrids because of the absence of male parent-specific bands. The results of hybrid identification provided solid evidence for further studies of hybrids and demonstrated SRAP molecular markers as a useful technology for assessing the purity of S. guianensis hybrids.
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Affiliation(s)
- C Q Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, 571737, Hainan, China,
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Zhu S, Liu T, Tang Q, Fu L, Tang S. Evaluation of bamboo genetic diversity using morphological and SRAP analyses. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414030132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Bajpai PK, Warghat AR, Sharma RK, Yadav A, Thakur AK, Srivastava RB, Stobdan T. Structure and Genetic Diversity of Natural Populations of Morus alba in the Trans-Himalayan Ladakh Region. Biochem Genet 2013; 52:137-52. [DOI: 10.1007/s10528-013-9634-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
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47
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Feng SG, Lu JJ, Gao L, Liu JJ, Wang HZ. Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China. Biochem Genet 2013; 52:127-36. [PMID: 24213846 DOI: 10.1007/s10528-013-9633-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.
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Affiliation(s)
- Shang-Guo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310018, China,
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Barzegar R, Peyvast G, Ahadi AM, Rabiei B, Ebadi AA, Babagolzadeh A. Biochemical systematic, population structure and genetic variability studies among Iranian Cucurbita (Cucurbita pepo L.) accessions, using genomic SSRs and implications for their breeding potential. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.03.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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He M, Wang Z. Genetic diversity of Hypericum perforatum collected from the Qinling Mountains of China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.03.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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ZHANG JS, WANG RG, YANG CY, WU C, SHI YW, WANG ZH, WANG Y, REN XL. Genetic Diversity of Agronomic Traits and Association Analysis with SRAP Markers in Flue-Cured Tobacco (<I>Nicotiana tabacum</I>) Varieties from China and Abroad. ACTA AGRONOMICA SINICA 2013. [DOI: 10.3724/sp.j.1006.2012.01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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