Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

Rakshit, Arunita; Rakshit, Sujay; Santhy, V.; Gotmare, Vinita; Mohan, Pratibha; Singh, Vikas; Singh, Shyam Bir; Singh, Jagdev; Balyan, H. S.; Gupta, P. K.; Bhat, S. R.

doi:10.1007/bf03263335

Cited by 12 publications

(7 citation statements)

References 24 publications

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“…PCR ampli cation was carried out in 15µl reaction using the touchdown PCR protocol in Veriti® 96 well Fast Thermal Cycler (Applied Biosystems). The PCR ampli cation programme (Rakshit et al 2010) consisted of an initial denaturation step at 94°C for 7 min (step-1), followed by 9 cycles (step-2) of 94°C for 15s, 65°C for 30s and 72°C for 60s with touch down by 1°C in each cycle from 65°C to 56°C followed by 40 cycles (step-3) of 94°C for 15s, 55°C for 30s and 72°C for 60s. Final extension was carried out at 72°C for 7 min (step-4).…”

Section: Methodsmentioning

confidence: 99%

WITHDRAWN: Microsatellite Marker Based DNA Fingerprinting of Cotton (Gossypium Spp.)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

Bargat

Venoor

et al. 2021

Preprint

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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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Section: Methodsmentioning

confidence: 99%

WITHDRAWN: Microsatellite Marker Based DNA Fingerprinting of Cotton (Gossypium Spp.)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

Bargat

Venoor

et al. 2021

Preprint

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“…Genome-wide allelic variation Among 300 SSR markers, 30 markers were not amplified whereas 32 were monomorphic and the remaining 208 were polymorphic in this experiment. We found only 69% of the markers revealing polymorphism among studied genotypes which is comparable to previous reports [3,5]. A total 208 polymorphic SSR markers were selected for genomewide allelic variation, among which 104 were present at the A and D, genomes, respectively.…”

Section: Resultssupporting

confidence: 87%

“…Previously, genetic diversity research in cotton was primarily based on morphological parameters. However, because of environmental interactions, uncertain genetic control of characteristics, and insufficient genome sampling for phenotypic characterization, morphological markers do not accurately explore genetic relationships among genotypes [3]. Available germplasm of cotton crop have several useful allelic variations that can be used to develop cultivars adapted to emerging environmental condition using traditional and genomic breeding methods also for fingerprinting genotypes because they are unaffected by the environment [5].…”

Section: Introductionmentioning

confidence: 99%

Genome –wide Allelic Variations and Population Structure Analysis of Cotton Genotypes using SSR Markers

Rehman¹,

Iqbal²

2022

PJBB

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The limited genetic base of modern cotton genotypes makes it difficult to improve cotton fibre yield and quality, emphasizing the necessity to study existing cotton germplasm resources. Therefore, this study was conducted to assess the genetic diversity and population structure of different cotton genotypes at DNA level. A total of 105 cotton genotypes were analyzed using 208 polymorphic SSR markers which were distributed on both A and D genomes. The total number of alleles in all genomes are 1382 Out of which 665 and 717 alleles were recorded in A and D genomes, respectively. In A genome, the maximum PIC values; 0.89 was observed for markers M92, M82 and M76 with the 10-total number of alleles exhibiting 100% polymorphism. These markers (M92, M82 and M76) located at the chromosomes 12A, 11A and 10A respectively with the estimation of 0.84 gene diversity. The highest PIC value 0.89 of D genome was detected for M191, M128 and M117 markers on 24D, 16D and 15D chromosomes with the 10 total numbers of alleles having the 0.84 values of gene diversity with 100% polymorphism. The UPGMA cluster DARWIN tree and Model-based Bayesian analysis clustered the studied cotton germplasm into four subpopulations, and the highest molecular variation revealed among subpopulations. Phylogenetic tree constructed for the whole germplasm population identified four major groups including; Group 1, Group 2, Group 3 and Group 4 consisting of 12, 21, 39 and 69 genotypes, respectively. Genetic distances among clusters clearly showed the variations among one another. SSR markers appear to be useful and reliable assets for future genetic and genomic analyses of cotton, such as genetic map construction, comparative genomic analyses, genetic diversity, and molecular marker-assisted breeding to select promising cotton genotypes, according to the current experiment.

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“…Compared to traditional morphological and biochemical identification, DNA identification has the advantages of being efficient and unaffected by environmental factors, and it has gradually become the most effective method for plant variety identification ( Liu et al 2015 ). The construction of fingerprints generally follows these principles: distinguishing all samples with as few primers as possible, reducing the experimental cost, reducing the heavy experimental work, and increasing the detection efficiency ( Liu et al 2017 , Rakshit et al 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic relationship analysis and molecular fingerprint identification of the tea germplasms from Guangxi Province, China

Guo

Xia

Cai³

et al. 2021

Breed. Sci.

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The tea plant ( Camellia sinensis ) is an evergreen woody plant with a high economic value. Guangxi Province is adjacent to the origin center of the tea plant in southern China. It has abundant germplasm resources and is a historically important tea-producing province. However, there is little information about the genetic diversity, genetic introgression, and fingerprints of the tea germplasms from Guangxi Province. Here, we constructed a phylogenetic tree of 126 tea accessions from Guangxi Province using 20 SSR markers. This tree classified these tea accessions into three subgroups containing 19, 47, and 60 members, respectively. High genetic similarity was observed among the three subgroups, and the genetic diversity of the populations was ranked as follows: subgroup 3 > subgroup 2 > subgroup 1. Furthermore, we analyzed the genetic relationships among 168 tea accessions from Guangxi Province and neighboring provinces. The results of the population structure analysis were highly consistent with the clustering results, and genetic introgression was observed. We identified six SSRs as the core marker set, because they could sufficiently distinguish between all 126 tea accessions. The results provide a crucial theoretical basis for utilization and protection of tea germplasms from Guangxi Province, and will help improve the breeding and popularization of elite tea cultivars.

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Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

Cited by 12 publications

References 24 publications

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

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

Genome –wide Allelic Variations and Population Structure Analysis of Cotton Genotypes using SSR Markers

Genetic relationship analysis and molecular fingerprint identification of the tea germplasms from Guangxi Province, China

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