Assessment of Genetic Diversity in Ziziphus mauritiana Using Inter-Simple Sequence Repeat Markers
01 Jan 2007-Journal of Plant Biochemistry and Biotechnology (Springer India)-Vol. 16, Iss: 1, pp 35-40
TL;DR: Morphologically similar but genetically distinct genotypes, identified using ISSR markers could be potential sources for genotype identification and to resolve controversies over misnomination of ber genotypes.
Abstract: Genetic diversity among 47 ber accessions belonging to cultivated species (Ziziphus mauritiana Lam) and one wild accession of Ziziphus nummularia (Burm F) Willed was investigated using Inter-Simple Sequence Repeat (ISSR) markers. A total of 167 amplification products were detected with 18 ISSR primers of which 152 (89.96%) were polymorphic. Most of the primers that produced distinct bands (14 primers out of 18) contained dinucleotide repeats. Primers based on (AC)n and (AG)n repeats produced more polymorphic bands. Genetic similarity ranging from 43.07% to 90.30% suggested that the 48 Ziziphus genotypes used in the study were divergent. Cluster analysis based on UPGMA method and Bootstrap analysis separated all the 48 genotypes in four distinct clusters. The present study has successfully distinguished morphologically similar genotypes that emphasize the use of molecular markers to the taxonomists. Morphologically similar but genetically distinct genotypes, identified using ISSR markers could be potential sources for genotype identification and to resolve controversies over misnomination of ber genotypes. Present study is the first report on the exploitation of ISSR markers in ber for genetic diversity analysis.
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TL;DR: A brief account of recent efforts to generate genomic resources for mango and its use in the analysis of genetic diversity and population structure of mango cultivars is presented.
Abstract: Mango (Mangifera indica L.) is known as the ‘king of fruits’ for its rich taste, flavor, color, production volume and diverse end usage. It belongs to plant family Anacardiaceae and has a small genome size of 439 Mb (2n = 40). Ancient literature indicates origin of cultivated mango in India. Although wild species of genus Mangifera are distributed throughout South and South-East Asia, recovery of Paleocene mango leaf fossils near Damalgiri, West Garo Hills, Meghalaya point to the origin of genus in peninsular India before joining of the Indian and Asian continental plates. India produces more than fifty percent of the world’s mango and grows more than thousand varieties. Despite its huge economic significance genomic resources for mango are limited and genetics of useful horticultural traits are poorly understood. Here we present a brief account of our recent efforts to generate genomic resources for mango and its use in the analysis of genetic diversity and population structure of mango cultivars. Sequencing of leaf RNA from mango cultivars ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ revealed substantially higher level of heterozygosity in ‘Amrapali’ over its parents and helped develop genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Sequencing of double digested restriction-site-associated genomic DNA (ddRAD) of 84 diverse mango cultivars identified 1.67 million high quality SNPs and two major sub-populations. We have assembled 323 Mb of the highly heterozygous ‘Amrapali’ genome using long sequence reads of PacBio single molecule real time (SMRT) sequencing chemistry and predicted 43,247 protein coding genes. We identified in the mango genome 122,332 SSR loci and developed 8,451 Type1 SSR and 835 HSSR markers for high level of polymorphism. Among the published genomes, mango showed highest similarity with sweet orange (Citrus sinensis). These genomic resources will fast track the mango varietal improvement for high productivity, disease resistance and superior end use quality.
27 citations
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TL;DR: High gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another, indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested.
Abstract: Genetic variation and relationships among 37 cultivars of Ziziphus mauritiana (Lamk.) native of India were analyzed using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. High level of polymorphism among SCoT (61.6%) and ISSR (61%) primers with higher PIC values ranging from 63.1 to 90.4% of SCoT and 47.3 to 88.8% of ISSR primers was recorded. SCoT and ISSR dendrograms revealed similarity coefficients ranging from 0.80 to 0.92 and 0.79 to 0.96, respectively, and clearly delineated all the cultivars of Z. mauritiana into well-supported distinct clusters. Greater Gst signifies higher amount of differentiation observed over multiple loci among seven Z. mauritiana populations. On the other hand, higher gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another. The genetic diversity of population 1 (Rajasthan) was the richest among all the seven populations. The largest genetic distance was measured between Maharashtra and West Bengal and the least between Rajasthan and Punjab cultivars. Most of the genetic diversity exists within population rather than among populations. Substantial variation in the ITS-1 region signifies its phylogenetic utility specifically in assessing genetic diversity in Z. mauritiana. The clustering patterns using three molecular marker systems vis-a-vis place of origin exhibited no consistency in grouping of Z. mauritiana cultivars as cultivars from the same place of origin were genetically cataloged into different SCoT, ISSR, and ITS phylogram clusters indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested.
20 citations
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TL;DR: This study detected genetic variation among 874 individuals from 31 natural populations covering the most representative distribution sites of sour jujube in China using nine simple sequence repeat markers to understand the genetic diversity and population structure of this species.
Abstract: Sour jujube or wild jujube (Ziziphus acidojujuba), considered as the ancestor of cultivated jujube, is an economically and ecologically important species. However, little is known about the population genetics of this species across China. In this study, we detected genetic variation among 874 individuals from 31 natural populations covering the most representative distribution sites of sour jujube in China using nine simple sequence repeat markers. By Bayesian, phylogenetic, and principal component analyses, two genetic groups of sour jujube in China were identified. One group was almost from east of the Taihang Mountains in the North China Plain, and the other was from west of the Taihang Mountains in the Loess Plateau. The high levels of genetic diversity (H
E = 0.659 and H
S = 0.674) was detected in these populations, and the moderate differentiation was found among populations (F
ST = 0.091, R
ST = 0.068, G′ST = 0.271). Populations from the North China Plain harbored higher genetic diversity (H
E = 0.686 and H
S = 0.706) than those from the Loess Plateau (H
E = 0.646 and H
S = 0.659) (P < 0.05). Analysis of molecular variance revealed that within-population genetic variation (88 %) was higher than that among populations (12 %). High gene flow (Nm = 6.572) and weak correlation between genetic and geographical distances (r
2 = 0.026, P > 0.05) suggested that gene flow occurred frequently among the populations. Understanding the genetic diversity and population structure could benefit germplasm conservation, genetic improvement, and systematic utilization of Ziziphus.
18 citations
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TL;DR: The obtained results demonstrate that the ISSR markers may be used for evaluation of the genetic diversity due to their efficiency in revealing polymorphism even in closely related germplasm and may help in Ziziphus genome analysis.
Abstract: Ziziphus spina-christi (sidr) is a shrub, sometimes a tree, native to a vast area of Africa stretching from Mauritania to West Africa. In the Kingdom of Saudi Arabia, it is an exotic medicinal plant for many diseases. The aim of this study was to assess the genetic diversity within and among 34 accessions of Z. spina-christi collected from different regions of Saudi Arabia. The amplification of genomic DNA with 11 inter-simple sequence repeat (ISSR) primers yielded 105 scorable loci, of which 93.4% were found to be polymorphic. The observed number of alleles (na), effective number of alleles (ne), Nei's gene diversity (h) and genetic diversity estimated by Shannon's information index (I) were 1.93, 1.44, 0.26 and 0.41, respectively. The total genetic diversity, Ht (0.266 ± 0.0289) was close to the average intrapopulation genetic diversity, Hs (0.2199 ± 0.0216). A high level of gene flow (Nm = 2.37) between populations, reflecting high genetic differentiation (Gst = 0.1739). The analysis of molecul...
17 citations
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TL;DR: Based on the presence of male parent-specific DNA fragment produced by RAPD and ISSR markers 13 out of 14 F1 progeny seedlings were found to be true hybrids and this is the first report in Z. mauritiana on the identification of true hybrids among F 1 progenies using molecular markers.
Abstract: Breeding in Ziziphus mauritiana Lam. through hybridization is limited by its small sized flowers, cross-incompatibility, low fruit-set and poor retention. In the present study, emasculation of flowers 2 h before anthesis and pollination by placement of dehisced flowers on stigma in inverted position resulted in increased fruit-set. Crossing of Z. mauritiana cultivars Gola and Thar Sevika (early maturity and fruit quality) with cultivars BS-1 (powdery mildew resistant) and Tikadi (fruit fly and frost tolerant) showed that Thar Sevika is cross compatible with BS-1 and Tikadi whereas Gola is cross compatible with BS-1 only. Among the crosses fruit-set range was 2.31–10.92%. Based on the presence of male parent-specific DNA fragment produced by RAPD and ISSR markers 13 out of 14 F1 progeny seedlings were found to be true hybrids. This is the first report in Z. mauritiana on the identification of true hybrids among F1 progenies using molecular markers.
7 citations
References
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TL;DR: A method is presented for the rapid isolation of high molecular weight plant DNA which is free of contaminants which interfere with complete digestion by restriction endonucleases, and which yields total cellular DNA.
Abstract: A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.
9,598 citations
Book•
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01 Jan 1996
TL;DR: This book discusses the genetic Basis of Quantitative Variation, Properties of Distributions, Covariance, Regression, and Correlation, and Properties of Single Loci, and Sources of Genetic Variation for Multilocus Traits.
Abstract: I. The Genetic Basis of Quantitative Variation - An Overview of Quantitative Genetics - Properties of Distributions - Covariance, Regression, and Correlation - Properties of Single Loci - Sources of Genetic Variation for Multilocus Traits - Sources of Environmental Variation - Resemblance Between Relatives - Introduction to Matrix Algebra and Linear Models - Analysis of Line Crosses - Inbreeding Depression - Matters of Scale - II. Quantitative-Trait Loci - Polygenes and Polygenic Mutation - Detecting Major Genes - Basic Concepts of Marker-Based Analysis - Mapping and Characterizing QTLs: Inbred-Line Crosses - Mapping and Characterizing QTLs: Outbred Populations - III. Estimation Procedures - Parent-Offspring Regression - Sib AnalysisTwins and Clones - Cross-Classified Designs - Correlations Between Characters - Genotype x Environment Interaction - Maternal Effects Sex Linkage and Sexual Dimorphism - Threshold Characters - Estimation of Breeding Values - Variance-Component Estimation with Complex Pedigrees - Appendices - Expectations, Variances and Covariances of Compound Variables - Path Analysis - Matrix Algebra and Linear Models - Maximum Likelihood Estimation and Likelihood-Ratio Tests - Estimation of Power of Statistical Tests -
6,525 citations
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TL;DR: The utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms.
Abstract: Simple sequence repeats (SSR), or microsatellites, are ubiquitous in eukaryotic genomes. Here we demonstrate the utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region. No sequencing is required to design the oligonucleotide primers. We tested primers anchored at 3' or 5' termini of the (CA)n repeats, extended into the flanking sequence by 2 to 4 nucleotide residues [3'-anchored primers: (CA)8RG, (CA)8RY, and (CA)7RTCY; and 5'-anchored primers: BDB(CA)7C, DBDA(CA)7, VHVG(TG)7 and HVH(TG)7T]. Radioactively labeled amplification products were analyzed by electrophoresis, revealing information on multiple genomic loci in a single gel lane. Complex, species-specific patterns were obtained from a variety of eukaryotic taxa. Intraspecies polymorphisms were also observed and shown to segregate as Mendelian markers. Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.
3,144 citations