Deciphering the unique SNPs among leading Indian tomato cultivars using double Digestion Restriction Associated DNA sequencing

World-wide grown and consumed tomato (Solanum lycopersicum) is used as model crop for newcultivar and fruit development. Genetic and genomic studieson Indian tomato cultivars will provide an insight that will enable development of breeding strategies and crop improvement. The present study aims to identifythe high quality common and unique SNPs and INDELs, present in 9 different Indian tomato cultivars using double digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 36.8 million raw reads were generated for selected cultivars and an average of 94% high-quality reads of each were uniquely aligned to the reference tomato genome (SLv3.0). Out of 6,957 SNPs and188 INDELs, we found 1,165 SNPs and 68 INDELs in genic regions. The genetic relationship among these cultivars suggested 4well-differentiated groups of cultivars. Similarly, 7 and 33 SNPs were identified in chloroplast and mitochondrial genomes of tomato. SNPs markers were identified for common and specific genes associated with different pathways and their gene ontology (GO) annotated. These SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to the research community, particularly, plant breeders, as a resource for SNP marker development.

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Deciphering the unique SNPs among leading Indian Tomato Cultivars using Double Digestion Restriction Associated DNA sequencing

10.1101/541227 ◽

2019 ◽

Cited By ~ 1

Author(s):

Reddaiah Bodanapu ◽

Sreehari V Vasudevan ◽

Sivarama Prasad Lekkala ◽

Navajeet Chakravartty ◽

Krishna Lalam ◽

...

Keyword(s):

Dna Sequencing ◽

Crop Improvement ◽

Genomic Research ◽

Variety Identification ◽

Nucleotide Polymorphisms ◽

Genetic Purity ◽

High Quality ◽

Purity Analysis ◽

Double Digestion ◽

Tomato Cultivars

World-wide grown and consumed tomato (Solanum lycopersicum) crop used as model system for new cultivar and fruit development. Genetic and genomic research of Indian tomato cultivars will provide an insight to develop new breeding strategies and crop improvement. The present study aimed to identify the high quality common and unique single nucleotide polymorphisms (SNPs), present in 9 different Indian tomato cultivars using double digestion restriction associated DNA sequencing (ddRAD-seq). Total of 36,847,092 raw reads (3.68 GB) were generated for all samples and 3,329,625 of high-quality reads were aligned uniquely to the reference tomato genome. Using stringent filtering, a total of 1,165 SNPs and 69 INDELs were found in genic regions, along with the unique variants to each cultivar was observed. Similarly, 7 and 33 variants were identified in chloroplast and mitochondrial genome of tomato. In addition, the population structure and genetic relationship among these cultivars suggested 4 well-differentiated sub-populations. Functional annotation of SNP/INDLEs associated with flanking sequences along with gene ontology and pathway analysis was performed. Identified SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to plant breeders and research community to deepen their understanding and enhance tomato breeding programs.

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SNP genotyping of maize (Zea mays) hybrids and parental inbred lines for genetic purity testing using double digest restriction site-associated DNA sequencing

Seed Science and Technology ◽

10.15258/sst.2021.49.3.02 ◽

2021 ◽

Author(s):

V. Satya Srii ◽

N. Nethra ◽

K. Umarani ◽

H.C. Lohithaswa ◽

Y.G. Shadakshari ◽

...

Keyword(s):

Zea Mays ◽

Dna Sequencing ◽

Restriction Site ◽

Crop Yields ◽

Indian Subcontinent ◽

Read Length ◽

Genetic Purity ◽

Maize Hybrids ◽

Maize Cultivars ◽

Purity Analysis

Maize (Zea mays) is the third major cereal crop in the Indian subcontinent, but the crop yields per hectare of Indian maize cultivars are less than half of the global average due to the impurity of seed lots supplied to farmers. In this study, we discovered high-quality Single Nucleotide Polymorphic markers (SNPs) in two widely cultivated maize hybrids and their parental inbreds. Paired-end double digest restriction site-associated DNA sequencing was used to discover SNPs and a total of 30,764,454 reads with a read length of 151 bp per sample were generated. Genotyping of SNPs for maize hybrids ‘MAH 14-5’ and ‘Hema’ revealed a total of 47,812 and 15,815 Genetic Purity Analysis markers, respectively, of which 44,388 and 12,391 were unique with 3,424 being common to both hybrids. Identified SNPs were used to develop primers for Kompetitive Allele-Specific PCR genotyping assays to determine the genetic purity of 10 seed lots and the results were found to correlate with Grow-out-Tests. Thus, the SNPs discovered in this study proved reliable to test the genetic purity of commercial seed lots. Advances in plant molecular breeding tools especially ddRADseq for SNP discovery offer new opportunities to genotype existing cultivars and accelerate the production of genetically pure seeds.

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De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽

10.3390/agronomy11071342 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1342

Author(s):

Shaghayegh Mehravi ◽

Gholam Ali Ranjbar ◽

Ghader Mirzaghaderi ◽

Anita Alice Severn-Ellis ◽

Armin Scheben ◽

...

Keyword(s):

De Novo ◽

Genetic Relationships ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genomic Resources ◽

High Quality Snps ◽

The Family ◽

Double Digestion ◽

Flanking Sequences ◽

Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

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Genetic purity analysis of cotton (Gossypium spp.) hybrids using SSR markers

Seed Science and Technology ◽

10.15258/sst.2010.38.2.09 ◽

2010 ◽

Vol 38 (2) ◽

pp. 358-366 ◽

Cited By ~ 5

Author(s):

P. Selvakumar ◽

R. Ravikesavan ◽

A. Gopikrishnan ◽

K. Thiyagu ◽

S. Preetha ◽

...

Keyword(s):

Ssr Markers ◽

Genetic Purity ◽

Gossypium Spp ◽

Purity Analysis

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Introduksi Gen DefH9-iaaM dan DefH9-RI-iaaM ke dalam Genom Tanaman Tomat Menggunakan Vektor Agrobacterium tumefaciens

Jurnal AgroBiogen ◽

10.21082/jbio.v6n1.2010.p18-25 ◽

2016 ◽

Vol 6 (1) ◽

pp. 18

Author(s):

Ragapadmi S Purnamaningsih

Keyword(s):

Acetic Acid ◽

Agrobacterium Tumefaciens ◽

Genetic Improvement ◽

Plant Cells ◽

Fruit Production ◽

Total Efficiency ◽

Parthenocarpic Fruit ◽

Tomato Genome ◽

Tomato Cultivars ◽

Indole 3 Acetic Acid

Introduction of DefH9-iaaM and DefH9-RI-iaaM Gene Into Tomato Genome Using Agrobacterium tumefaciens. Ragapadmi Purnamaningsih. Plant genetic improvement can be conducted through genetic engineering. Parthenocarpic fruit production could increase fruit production and its qulities. IAA genes were introduced into three tomato cultivars Ratna, Opal and LV 6117 using two constract genes DefH9-iaaM and DefH9-RI-iaaM. The iaaM gene is able to increase auxin biosynthesis in transgenic plant cells and organs because indol-eacetamide, synthesized by the product of the iaaM gene, is converted either chemically or enzimatically to indole-3-acetic acid (IAA), while the promotor DefH9 enable IAA gene expressed specifically in the ovules. The objectives of this experiment was to identify gene introduction into plant genom of three tomato cultivars. The factors tested were two constract of IAA genes (DefH9-iaaM or DefH9-RI-iaaM), tomato cultivars (Ratna, Opal, and LV 6117) and time of explant inoculation (5, 15, 30 minute). The result showed that the best time inoculation was 5 minute. Otherwise three tomato cultivars response better to DefH9-RI-iaaM than DefH9-iaaM. The total efficiency of regeneration and total efficiency of transformation of both genes were 25.38% and 20.32%. PCR analysis showed that 10 plant have positive PCR, were 1 plant carried (Opal) DefH9-iaaM gene and 9 plant (Ratna, Opal, LV 6117) carried DefH9-RI-iaaM gene.

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A rapid method for isolating high quality plasmid DNA suitable for DNA sequencing

Nucleic Acids Research ◽

10.1093/nar/18.24.7463 ◽

1990 ◽

Vol 18 (24) ◽

pp. 7463-7464 ◽

Cited By ~ 41

Author(s):

D. Stephen ◽

C. Jones ◽

J.Paul Schofield

Keyword(s):

Dna Sequencing ◽

Rapid Method ◽

Plasmid Dna ◽

High Quality

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Genetic purity certificate in seeds of hybrid maize using molecular markers

Revista Brasileira de Sementes ◽

10.1590/s0101-31222006000100024 ◽

2006 ◽

Vol 28 (1) ◽

pp. 169-175 ◽

Cited By ~ 5

Author(s):

Kalinka Carla Padovani de Carvalho Salgado ◽

das Graças Guimarães Carvalho Vieira ◽

Édila Vilela de Resende Von Pinho ◽

Cláudia Teixeira Guimarães ◽

Renzo Garcia Von Pinho ◽

...

Keyword(s):

Isocitrate Dehydrogenase ◽

Female Parent ◽

Parental Line ◽

Maize Breeding ◽

Genetic Purity ◽

Mendelian Segregation ◽

Purity Analysis ◽

Young Leaves ◽

Parental Lines ◽

Hybrid Maize

One of the main features that confer high quality to the seed is its genetic purity, in which one of the major causes of contamination is the self-pollination of the female parent. Up to date, there is no accurate and fast methods for detecting such contamination. Thus, this work was carried out to certify the genetic purity in seeds of hybrid maize using different biochemical and DNA-based markers. Two single-cross hybrids and their parental lines derived from the maize breeding program at UFLA were evaluated by isoenzymatic pattern of alcohol dehydrogenase (ADH), esterase (EST), acid phosphatase (ACP), glutamate-oxaloacetate transaminase (GOT), malate dehydrogenase (MDH), isocitrate dehydrogenase (IDH), phosphoglucomutase (PGM), 6-phosphoglucomate dehydrogenase (PGDH), catalase (CAT) and ß-glucosidade (ßGLU) and by microsatellites markers. The enzymatic systems that were able to distinguish the hybrids from their parental line were the catalase, the isocitrate dehydrogenase and the esterase. The esterase showed a Mendelian segregation pattern for UFLA 8/3 hybrid, that enables a safer genetic purity certificate. Microsatellites were able to differentiate the hybrid lines and the respective parental lines. Moreover, this technique was fast, precise and without environment effects. For microsatellites, the amplification pattern was identical when young leaves or seeds were used as DNA source. The possibility of using seeds as DNA source would accelerate and facilitate the role process of the genetic purity analysis.

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COMMERCIAL PRODUCTION OF HIGH QUALITY HYBRID ASPARAGUS SEED WITH HIGH GENETIC PURITY

Acta Horticulturae ◽

10.17660/actahortic.1999.479.55 ◽

1999 ◽

pp. 407-414 ◽

Cited By ~ 1

Author(s):

S. Walker ◽

Lon K. Inaba ◽

S. A. Garrison ◽

C. Chin ◽

W. Odermott

Keyword(s):

Commercial Production ◽

Genetic Purity ◽

High Quality

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Genetic purity analysis of hybrid broccoli (Brassica oleracea var. italica) seeds using RAPD PCR

Australian Journal of Agricultural Research ◽

10.1071/ar01022 ◽

2002 ◽

Vol 53 (1) ◽

pp. 51 ◽

Cited By ~ 6

Author(s):

Phillip A. Crockett ◽

Mohan B. Singh ◽

C. K. Lee ◽

Prem L Bhalla

Keyword(s):

Plant Size ◽

Vegetable Crops ◽

Genetic Purity ◽

F1 Hybrid ◽

Shoot Ratio ◽

Root Shoot Ratio ◽

Rapd Pcr ◽

Purity Analysis ◽

Hybrid Seeds ◽

Contrast Response

Determination of genetic purity of F1-hybrid seeds is aquality control requirement in the production of hybrid Brassica vegetableseeds. Hybrid varieties of these vegetable crops have arisen from a limitedgermplasm base, making discrimination of parental and hybrid lines verylaborious and troublesome. The use of RAPD PCR for evaluating seed purity in acommercial F1-hybrid broccoli a single cultivar bywithholding water. In Expt 2, plants of EP and MK were grown together in thesame container and received water daily with gradation in intensity of waterdeficit achieved by varying the daily water ration per container.All cultivars in each experiment exhibited commonly reported responses towater deficit, characterised by diminished evaporative surface area andincreased root : shoot ratio. The response of MK was primarily morphologicaland MK plants had smaller plant size, higher root : shoot ratio, and a lowergrowth rate compared with temperate cultivars. By contrast, response oftemperate cultivars was primarily physiological; stomatal conductance oftemperate cultivars was lower and these cultivars had a greater tendency forleaf lamina osmotic a

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Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

Jurnal AgroBiogen ◽

10.21082/jbio.v11n2.2015.p49-58 ◽

2016 ◽

Vol 11 (2) ◽

pp. 49

Author(s):

Andari Risliawati ◽

Eny I. Riyanti ◽

Puji Lestari ◽

Dwinita W. Utami ◽

Tiur S. Silitonga

Keyword(s):

Ssr Markers ◽

Ssr Marker ◽

Variety Identification ◽

Polymorphism Analysis ◽

Dna Fingerprints ◽

Soybean Variety ◽

Genetic Purity ◽

Electrophoresis System ◽

Simple Sequence ◽

Genetic Analyzer

Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested, but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles, frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e. Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.

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