Microsatellite Marker Based DNA Fingerprinting of Cotton (Gossypium Spp.) Hybrids and Their Parents

Abstract Cotton production in India by vast majority comes from cotton hybrids whose genetic purity is of great significance in seed production chain and trade. Therefore, there is need to develop a rapid, reliable and reproducible technique to assess the genetic purity of cotton hybrids as traditional, morphological traits-based ‘Grow-Out Test’ is resource intensive, time consuming, tedious and not an infallible procedure. In this regard, a study was planned to understand the genetic diversity among the hybrids and their parents, and also to identify SSR markers for confirmation of genetic purity or hybridity. One intra-arboreum hybrid, CICR2 (DS 5 GMS × LD 327 Sel.), four intra-hirsutum hybrids viz., CSHH198 (CSH 19 × CSH 8), CSHH238 (SH 2379 9Y × PIL 8 Sel.), CSHH243 (CSH 2013 × CSH 43), CSHH1862 (GMS 16A × CB 33) and one hirsutum × barbadense hybrid, Phule 388 (RHC-006 × RHCb-001) along with their respective parental lines were selected for molecular characterization. Of the total 215 SSR markers surveyed, 60 markers conveyed polymorphism. The information conveyed by the polymorphic SSR markers was utilized to assess the molecular divergence among the study material. Maximum genetic dissimilarity of 0.66 was noted between Phule 388 and LD 327 (Sel.), and between RHC-006 and DS 5 (GMS). Minimum genetic dissimilarity of 0.07 was observed between CSHH1862 with CB 33, followed by 0.11 between CICR2 with DS 5 (GMS). SSR markers were highly efficient in capturing both intra-species and inter-species level diversity. The clustering and factorial analysis was in congruence with the species of Gossypium. The diploid species genotypes were clustered separately and distinctly from the rest of the genotypes. All the hirsutum hybrids and their respective parents were found closely clustered. The inter-specific hybrid, Phule 388 along with its parents was found grouped closely. The genetic purity of the hybrids was confirmed using identified SSR markers [GH486, BNL1421, BNL3594, JESPR151 for G. hirsutum hybrid CSHH198; GH486, BNL2449, JESPR151, TMB0436 for G. hirsutum hybrid CSHH238; BNL2449, JESPR151, JESPR152 for G. hirsutum hybrid CSHH243; and, GH527, BNL3812, TMB1484, TMB1645, NAU1190, BNL3816 for inter-specific G. hirsutum × G. barbadense hybrid Phule 388]. The SSR markers were efficient in analysis of hybrid seed purity. The information generated in the present study about genetic diversity and genetic purity testing will greatly facilitate quality seed production of these cotton hybrids and thus, better cotton production.

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DNA fingerprinting and genetic purity testing of a new broccoli hybrid using SSR markers

Seed Science and Technology ◽

10.15258/sst.2013.41.3.13 ◽

2013 ◽

Vol 41 (3) ◽

pp. 464-468

Author(s):

H.F. Yu ◽

J.S. Wang ◽

Z.Q. Zhao ◽

X.G. Sheng ◽

H.H. Gu

Keyword(s):

Dna Fingerprinting ◽

Ssr Markers ◽

Genetic Purity ◽

Purity Testing

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Genetic diversity of walnut (Juglans regia L.) seedlings through SSR markers in north-western Himalayan region of Jammu

Bangladesh Journal of Botany ◽

10.3329/bjb.v49i4.52517 ◽

2020 ◽

Vol 49 (4) ◽

pp. 1003-1012

Author(s):

Rafiq Ahmad Shah ◽

Parshant Baksi ◽

Amit Jasrotia ◽

Deep JI Bhat ◽

Rucku Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Decision Making ◽

Ssr Markers ◽

Juglans Regia ◽

Germplasm Management ◽

Expected Heterozygosity ◽

Western Himalayan Region ◽

Ssr Primers ◽

Genetic Dissimilarity ◽

North Western

screening of 25 SSR markers, revealed 23 clear and consistent amplification profiles in the entire walnut germplasm set. A total of 54 alleles were amplified by SSR primers and the number of alleles range from 2 to 3. The PIC value ranged from 0.36 to 0.68. The dendrogram classified all genotypes into two main clusters with various degrees of subclustering. Estimated genetic dissimilarity coefficient ranged from 0.36 to 0.85. Through model-based cluster analysis all genotypes were grouped into 5 genetically distinct subpopulations. The expected heterozygosity at a given locus was found to range from 0.520 to 0.5477. Similarly, population differentiation measurements (Fst) ranged from 0.2286 to 0.2909. These findings would be helpful for decision making in future walnut breeding studies, germplasm management activities to maximize genetic diversity in walnut germplasm and may also prove useful in future for conducting association mapping in walnut for different traits.

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Development of EST–SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids

Genome ◽

10.1139/g11-033 ◽

2011 ◽

Vol 54 (8) ◽

pp. 684-691 ◽

Cited By ~ 15

Author(s):

B. Pranavi ◽

G. Sitaram ◽

K.N. Yamini ◽

V. Dinesh Kumar

Keyword(s):

Ssr Markers ◽

Castor Bean ◽

Expressed Sequence Tag ◽

Ricinus Communis ◽

Rapid Development ◽

Genetic Purity ◽

Ricinus Communis L ◽

Purity Testing ◽

Expressed Sequence ◽

Simple Sequence

Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST–SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.

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Genetic purity testing of loose-curd cauliflower hybrids using SSR markers and grow out test

Seed Science and Technology ◽

10.15258/sst.2012.40.2.06 ◽

2012 ◽

Vol 40 (2) ◽

pp. 209-214 ◽

Cited By ~ 9

Author(s):

Z. Zhao ◽

H. Gu ◽

X. Sheng ◽

H. Yu ◽

J. Wang ◽

...

Keyword(s):

Ssr Markers ◽

Genetic Purity ◽

Purity Testing

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Identification and utilization of informative EST-SSR markers for genetic purity testing of coconut hybrids

Journal of Plantation Crops ◽

10.19071/jpc.2016.v44.i2.3101 ◽

2016 ◽

Vol 44 (2) ◽

Cited By ~ 1

Author(s):

P.Preethi, M.K.Rajesh, C.U.Rahul, B.A. Jerard, K. Samsudeen ◽

R.J. Thomas A. Karun

Keyword(s):

Ssr Markers ◽

Morphological Traits ◽

Transcriptome Data ◽

Genetic Purity ◽

Breeding Programs ◽

Purity Testing ◽

Leaf Transcriptome ◽

Parental Lines

Coconut palms are categorized into two forms, viz., ‘talls’ and ‘dwarfs’ which are being utilized to produce hybrids through the process of inter-varietal or intra-varietal crosses. Hybrid coconut seedlings are generally identified and selected based on morphological traits by plant breeders, which is quite difficult and requires expertise. Even minor errors in identification may adversely affect breeding programs in coconut, which is spread over many decades. In this study, we have utilized thirty EST-SSR markers, derived from existing coconut leaf transcriptome data, for screening polymorphism between eighteen coconut parental lines. The polymorphic primers capable of differentiating the parental palms were then utilized successfully for assessment of purity of hybrids derived from these parents. Thus, the current study demonstrates the utility of EST-SSR markers in determining the genetic purity of hybrids in coconut.

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DNA fingerprinting of foxtail millet (Setaria italica L.) variety ATL 1 using SSR and RAPD markers along with morphological descriptors

Tropical Plant Research ◽

10.22271/tpr.2020.v7.i3.072 ◽

2020 ◽

Vol 7 (3) ◽

pp. 587-593

Author(s):

Senthil Natesan ◽

◽

Gowtham Murugesan ◽

Nandhini Murugan ◽

Sarankumar Chandran ◽

...

Keyword(s):

Dna Fingerprinting ◽

Ssr Markers ◽

Rapd Markers ◽

Plant Genetic Resources ◽

Foxtail Millet ◽

Setaria Italica ◽

National Bureau ◽

Genetic Purity ◽

Purity Testing ◽

Ssr Primers

Foxtail millet (Setaria italica) is a cultivated nutritional cereal, which originated in South Asia and is considered one of the oldest cultivated millets in India. DNA fingerprinting is mandatory for registration of newly developed varieties with National Bureau of Plant Genetic Resources (NBPGR) and Protection of Plant Varieties and Farmers' Rights Authority (PPV&FRA). Due to the limited availability of genomic information in foxtail millet, the use of DNA based markers in fingerprinting of crop varieties is also limited. Hence in the present investigation, available RAPD and SSR markers of cereals are used for fingerprinting the foxtail millet varieties. The newly released variety ATL 1 is differentiated from popular variety CO (Te) 7 using SSR and RAPD markers. About 66 maize SSR primers, 16 sorghum SSR primers, and 10 RAPD primers were used in the study. Out of 66 maize SSR markers used for study, one showed polymorphism. The marker umc1704 showed polymorphism between CO (Te) 7 and ATL 1 by the presence of 670 bp allele CO (Te) 7. The RAPD primers OPB4, OPA5, OPA11 and OPB1 also helped for differentiation of the two varieties. The identified makers will help for genetic purity testing of CO (Te) 7 and ATL 1 in the seed chain.

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