Molecular diversity analysis and DNA fingerprinting of cotton varieties of India

Santhy, V.; Meshram, Mithila; Santosh, H. B.; Kranthi, K. R.

doi:10.31742/ijgpb.79.4.10

Cited by 5 publications

(8 citation statements)

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“…The higher polymorphism per cent observed in the present study might be due to inclusion of different species of cotton in the study. In our earlier diversity studies, 16 and 27 per cent SSR polymorphism was observed in G. arboreum (Santosh et al, 2020) and tetraploid cotton (Santhy et al, 2019), respectively. Earlier, Selvakumar et al (2010) observed 30 per cent polymorphism during genetic purity analysis of three cotton hybrids using SSR markers.…”

Section: Resultsmentioning

confidence: 65%

“…The genetic similarity of 0.85 was noted between intra-hirsutum hybrid, CSHH243 and its male parent CSH 2013, and between intra-hirsutum hybrid, CSHH1862 and its female parent GMS 16A, and between GMS 16A and CB 33. The SSR markers were highly efficient in capturing both intra-species and inter-species diversity (Abd El-Moghny et al, 2017;Santhy et al, 2019;Santosh et al, 2020) as they revealed higher genetic diversity between different species and lesser diversity within species or between hybrids and their parents.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, SSR based clustering is known to have a better correlation with the pedigree than the dendrogram from morphological data (Giancola et al, 2002). and unambiguous cultivar identification and differentiation (Santhy et al, 2019;Santosh et al, 2020). The present study has identified polymorphic SSR markers which can be used in hybrid purity testing.…”

Section: Table 1 List Of Hybrids Along With Their Parentage and Salie...mentioning

confidence: 86%

“…These molecular markers precisely assess the genotype, and not the phenotype (Sundaram et al, 2008). Among these markers, SSR markers are widely preferred for genetic purity testing (Saravanan et al, 2007;Selvakumar et al, 2010;Menka et al, 2016, Bora et al, 2016Ben Romdhane et al, 2018), DNA fingerprinting (Santhy et al, 2019;Santosh et al, 2020), genetic diversity analysis (Abd El-Moghny et al, 2017) apart from other plant breeding applications owing to their reproducibility, co-dominant inheritance, genome-wide presence, robustness, higher polymorphism and analytical simplicity (Rakshit et al, 2011). Therefore, this study was planned to understand the genetic diversity among the hybrids and their parents and to identify SSR markers for confirmation of genetic purity or hybridity.…”

Section: Introductionmentioning

confidence: 99%

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Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

2022

EJPB

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Cotton production in India by the vast majority comes from cotton hybrids whose genetic purity is of great significance in the seed production chain and trade. Therefore, there is a need to develop a rapid, reliable and reproducible technique to assess the genetic purity of cotton hybrids as the 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 and CB 33, followed by 0.11 between CICR2 and DS 5 (GMS). SSR markers were highly efficient in capturing both intra-species and inter-species level diversity. The clustering and factorial analysis were 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 hybrids, CSHH198; GH486, BNL2449, JESPR151, TMB0436 for G. hirsutum hybrids, 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 the 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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Section: Resultsmentioning

confidence: 65%

Section: Resultsmentioning

confidence: 99%

Section: Table 1 List Of Hybrids Along With Their Parentage and Salie...mentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

2022

EJPB

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“…However, artificial selection for a few traits in cotton germplasm by traditional breeding methods has resulted in narrow genetic diversity among cotton varieties. Consequently, the relatively narrow genetic base restricts the progress of the cotton breeding ( Zhang et al., 2008 ; Saleem et al., 2020 ; Santhy et al., 2019 ; Zhang et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton

Liu

Zhao²,

Geng³

et al. 2023

Front. Plant Sci.

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Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were “hotspot” mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.

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Molecular Techniques for Testing Genetic Purity and Seed Health

Santhy

Sandra

Ravishankar

et al. 2023

Seed Science and Technology

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With the globalization of seed trade and transgenic variety development, the application of molecular technologies for seed quality gained more significance in both the internal and international markets. Besides germination, genetic purity and seed health are the two most important seed quality parameters that determine the planting value of a seed lot. Compared to the conventional methods of testing, molecular marker technologies are more efficient for quality analysis as these are more accurate, robust, abundant, and faster. Among the various markers, simple sequence repeats (SSRs), due to their genome-wide presence, reproducibility, multi-allelic nature, and co-dominant inheritance, have emerged as the best markers, for establishing varietal distinctness, identity, and variety/hybrid seed purity testing. With the advent of the next-generation sequencing (NGS) technology, single nucleotide polymorphic (SNP) markers also became widely popular, and the closest to being an ideal marker besides SSRs, in seed genetic purity testing. With large-scale GM crop cultivation, testing for the adventitious presence and trait purity are two added components of seed quality testing. The methods of GM seed quality testing include DNA-based (conventional and real-time PCR), protein-based (lateral flow test and ELISA), and bioassay-based technologies. DNA-based methods including PCR/real-time PCR assays have been successfully employed to detect the adventitious presence of transgenic seeds in seed trade especially at international level, as well as in the national gene banks for germplasm conservation. ISTA plays a prominent role in international harmonization and providing universal guidelines on use of different methods to detect GM seeds. The BMT group of UPOV and the Working Group on DNA Methods of the Variety Committee of ISTA, work in tandem to standardize suitable molecular techniques for establishing variety identity and purity testing, respectively. In the area of seed health testing also, molecular detection assays such as, PCR (nested PCR, multiplex PCR, real-time PCR), loop-mediated isothermal amplification (LAMP), and DNA microarray with many advantages over the conventional assays have been proven highly useful. However, there is a need to validate the usefulness of molecular markers through stringent multi-laboratory tests for their reproducibility before recommending them in routine seed purity and health testing.

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Molecular diversity analysis and DNA fingerprinting of cotton varieties of India

Cited by 5 publications

References 0 publications

Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton

Molecular Techniques for Testing Genetic Purity and Seed Health

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