AFLP Primer Pairs Research Articles

Genetic Diversity among Single, Double, And Triple Cross Hybrids in Beit Alpha Cucumber (Cucumis sativus)

Genetic variation was investigated in fifteen single, eighteen three-way, and nine double hybrid crosses and their parents along with nine elite commercial cucumber hybrids. Six lines (NS5, NS9, NS17, NS29, NS31, and NS33) were used to develop these cross hybrids. Based on AFLP and SSR analysis, the studied cucumber genotypes have a narrow genetic base. The results also showed genetic differentiation compared to commercial varieties. Out of 1352 bands produced from 12 AFLP primer pairs, only 47 were polymorphic. Similarly, out of 26 SSR primers, only one primer was polymorphic. The highest heterozygosity index (0.6044), polymorphic information content value (0.5392), and marker Index (0.6044) were observed with M-CTT_E-AAG AFLP primer combination, while the highest effective multiplex ratio (2.8246) and resolving power (4.8421) were observed with M-CTC_E-AGC AFLP primer combination. Genetic distance estimation revealed clear distinctiveness of the studied genotypes with the control varieties. The cluster analysis by UPGMA showed two main clusters covering 84% of the studied genotypes grouped. This research shows that double and three-way hybrid crosses can be used in cucumber hybrid breeding.

Ocena wzrostu i stabilności genetycznej agrestu (Ribes grossularia L.) rozmnażanego in vitro oraz ex vitro

Celem badań była ocena fenotypowa i genetyczna roślin 15 genotypów agrestu, rozmnożonych in vitro oraz ex vitro przez sadzonki zielne, uprawianych drugi rok warunkach polowych. Silniej rosły krzewy rozmnożone in vitro. Ich wysokość i liczba pędów były istotnie większe dla 11 genotypów, a szerokość dla 12 genotypów agrestu. Krzewów, na których pojawiły się owoce było znacznie więcej u roślin mnożonych tradycyjnie. Przeprowadzono analizę stabilności genetycznej klonów pochodzących z kultur in vitro pięciu odmian agrestu. Analizowano 13‒15 roślin z in vitro oraz rośliny mateczne. Liczba produktów generowanych przez pary starterów AFLP wahała się od 33 do 108. Najwyższą całkowitą liczbę produktów amplifikacji uzyskano w wyniku reakcji AFLP dla roślin ‘Hinnonmaki Rot’ (300), a najmniejszą dla odmiany ‘Hinsel’ i ‘Resika’ (262). Zmienność genetyczna w roślinach agrestu in vitro wahała się od 1,03% dla ‘Captivator’ do 10,3% w przypadku ‘Hinsel’. Stabilność genetyczną oceniano także przy użyciu markerów ISSR. Wykorzystano rośliny 5 genotypów pochodzące z rozmnażania tradycyjnego oraz in vitro. Uzyskano łącznie 2294 produktów amplifikacji, z czego 2,8% było polimorficznych. Wielkość otrzymanych produktów wynosiła od 250 do 2900 pz, w zależności od startera i odmiany. Analiza ISSR-PCR wskazała na różny stopień polimorfizmu – od 0 dla ‘Hinnonmaki Rot’ i ‘Resica’ do 11,6% dla odmiany ‘Hinsel’.

Genetic impacts of habitat loss on the rare Banded Ironstone Formation endemic Ricinocarpos brevis (Euphorbiaceae)

Ricinocarpos brevis (Euphorbiaceae) is a declared rare species currently known from only three Banded Ironstone Formation (BIF) ranges (Perrinvale, Johnston and Windarling Ranges) in the Yilgarn region of Western Australia. The present study assessed the potential impact of proposed mining on genetic diversity within R. brevis. Approximately 30 plants were sampled from each of 14 sites across the known distribution of R. brevis. Genetic variation and its spatial structure was assessed with 144 polymorphic AFLP markers that were generated by two independent primer pairs: M-CTG/P-AC (81 markers) and M-CTA/P-AC (63 markers). Hierarchical spatial genetic structure was assessed by an analysis of molecular variance (AMOVA), Mantel tests of association between genetic- and geographic-distance and ordination. Specific attention was given to the extent of genetic differentiation of the three populations on the Windarling Range W4 deposit, which was proposed for mining operations. Strong genetic differentiation (ΦPT=0.186–0.298) among the three ranges was found. Genetic differentiation of the Johnston Range populations from Windarling and Perrinvale was greater than expected under isolation by distance predictions, suggesting adaptive genetic differentiation driven by site environmental differences, reflected by differences in plant community, substrate and landscape features. In contrast, genetic differentiation among the three Windarling Range regions (W2, W3, W4) was weaker (ΦPT=0.055–0.096). Mean pairwise ΦPT=0.078 for the 10 Windarling sites, which was unchanged with the removal of the W4 populations. In addition, none of the markers scored were unique to the W4 populations. Thus, for this set of markers, the removal of plants on the Windarling Range W4 deposit had little impact on genetic diversity within R. brevis. Strong concordance in results from the independent datasets generated by the two AFLP primer pairs provides overall support for the conclusions drawn.

Mating System and Genetic Variability of the Endangered Endemic Aquatic Lycophyte,Isoëtes yunguiensis, in China Determined using AFLP Markers

In this study, mating system, genetic diversity, and genetic structure of the endangered endemic aquatic lycophyte Isoëtes yunguiensis in China was investigated using AFLP markers. The estimates of outcrossing rates (tm = 1.200) indicate that diploid I. yunguiensis is a predominantly outcrossing species. Six selected AFLP primer pairs used in the study amplified 195 reproducible bands, 160 of which were polymorphic (PPB = 82.05%), indicating significant genetic diversity at the species level. AMOVA revealed that 40.12% of the genetic variation was attributable to differences between populations and the rest (59.88%) to variability within populations. High outcrossing rates and the historical accumulation of genetic variation may be responsible for the high levels of genetic diversity observed in the I. yunguiensis population. To maintain the current level of genetic diversity for this species, we recommend increasing in situ conservation sites.

Seed coat thickness differentiation and genetic polymorphism for lupinus mutabilis sweet breeding

The paper investigates seed coat characteristics in L. mutabilis, a potential forage crop. In the study twelve genotypes, including three epigonal lines KW-5, KW-10, Pop.1 and lines with traditional type of growth XM.5, Pop.15 LM.13, LM.34, ‘Potosi’, Mut-45, Mut-160, Mut-136, Mut-628 were evaluated. The highest seed coat percentage was recorded in mutant line Mut-160 and the lowest was noted for mutant line Mut-45. The statistical significance relationship between seed coat thickness and 1000 seeds weight was not notice. It’s gives capabilities for selection of favorable genotypes in breeding process. In order to illustrate genetic diversity among the genotypes tested, 24 ISSR primers and 6 pairs of AFLP primers were used. They generated a total of 685 polymorphic amplification products in 12 evaluated Andean lupin genotypes. The products characteristic only for the finest seed coat lines Mut-45 were detected as well as for the thickness seed coat line Mut-160.

Genetic diversity, population structure and marker trait associations for alkaloid content and licit opium yield in India-wide collection of poppy (Papaver somniferum L.)

The importance of alkaloids of opium poppy is increasing constantly worldwide to fulfill the demand of pharmaceutical industries. India is one of the countries to produce gum opium and contain many potential genotypes to attend the recent demand of alkaloids. So, for proper utilization of the available potential genotypes, the present investigation was carried out to study the genetic diversity and genetic differentiation along with marker-trait association based on quantitative traits as well as AFLP marker in a large number of germplasm lines of opium poppy which were collected from different parts of India. Various genetic parameters and correlation among different traits were also worked out to find out the particular traits enhancing yield potential. Eight AFLP primer pairs were deployed that generated 140 polymorphic bands with fragment ranging in size from 50 to 498bp in size. The maximum gene diversity was found in the germplasm lines of UP. Most of the variability (96%) was partitioned into within populations implying that collection strategies for conservation should focus on a few populations with many individuals across the ecological amplitude of the population. Genetic differentiation was FST=0.0413, that implies more or less complete panmixis. The morphine was found associated with seven AFLP loci, such as E-AAG/M-CAG_76, E-AAC/M-CAG_102, E-ACT/M-CTA_181, E-ACG/M-CTC_167, E-ACG/M-CTC_176, E-ACG/M-CTC_194, and E-ACG/M-CTC_102 which showed stability by both models (GLM, MLM) of analysis while three markers (E-ACT/M-CAA_53,E-ACT/M-CAA_243,E-AGG/M-CTG_241) for codeine, four markers (E-ACT/M-CAA_193,E-AAC/M-CAG_151, E-AAC/M-CAG_91, and E-AGC/M-CTA_75) for thebaine, six for narcotine (E-ACT/M-CAA_85, E-AGG/M-CTG_75, E-AAC/M-CAG_116, E-ACT/M-CTA_122, E-ACT/M-CTA_182, and E-ACT/M-CTA_209), two markers (E-AAG/M-CAG_303, and E-AAC/M-CAG_210) for papaverine and five markers (E-ACT/M-CAA_76, E-AAG/M-CAG_122, E-AAG/M-CAG_245, E-AGG/M-CTG_84, and E-AGG/M-CTG_219) for opium yield were found associated (P<0.05). This is first report on population genetic structure and differentiation in India-wide collection of opium poppy. Based on both marker analysis, the germplasm lines BR296, BR061, BR059 and BR282 were identified utmost diverse for developing mapping populations to carry out linkage/QTL mapping of opioids in poppy. Simultaneously, these lines can also be used in multi-parent breeding program to develop new variety with targeted multi-traits. The associated AFLP markers for various alkaloids open the new avenues for alkaloid improvement breeding program with MAS, genome-wide association and QTL analysis.

Association mapping for identification of ISSR and AFLP markers linked with resin yield in Himalayan Chir Pine (Pinus roxburghii Sarg

AbstractIn Pinus roxburghii, marker-trait associations were studied for resin yield using a set of 238 DNA based markers derived from 9 ISSR and 5 AFLP primer pairs. A total of 240 genotypes of P. roxburghii from a natural population in Chakrata division (Tiunee range), Uttarakhand (India) were evaluated for resin yield. Based on stable resin production in consecutive years, 53 genotypes that were best representatives of the variation in resin yield (0.25 to 8.0 kg/tree/year) were used for genotyping and association analysis. For carrying out the association studies, two approaches were used. First, using simple linear regression, resin yield was regressed on all 238 available polymorphic markers (148 ISSR markers and 90 AFLP markers) and second, evidence for association was examined applying population structure information using STRUCTURE and STRAT to avoid any spurious associations between a candidate marker and phenotype. In regression analysis, 16 ISSR and 12 AFLP markers showed significant association with resin yield. In the second approach, 18 ISSR and 18 AFLP loci were found to be associated with resin yield in the absence of population structure out of which 2 ISSR and 3 AFLP loci were common with those associated in regression analysis. After accounting for population structure, 38 ISSR, and 3 AFLP loci revealed association out of which one ISSR and one AFLP locus was found to be common with both simple linear regression and test of association in the absence of population stratification. There was no obvious correlation between population structure and resin yield.

An AFLP marker linked to the leaf rust resistance gene LrBi16 and test of allelism with Lr14a on chromosome arm 7BL

Leaf rust (LR), caused by Puccinia triticina, is one of the most widespread diseases of common wheat (Triticum aestivum L.) worldwide. The LR resistance gene LrBi16 has been mapped on chromosome arm 7BL in Chinese wheat cultivar Bimai 16 and was closely linked to SSR loci Xcfa2257 and Xgwm344 with genetic distances of 2.8cM and 2.9cM, respectively. In the present study, a total of 304 AFLP primer pairs were used to screen Bimai 16 and Thatcher and resistant and susceptible DNA bulks. The polymorphic AFLP marker P-ATT/M-CGC173bp was used to genotype F2 and F3 populations to identify markers more closely linked to LrBi16. Marker P-ATT/M-CGC173bp was tightly linked to LrBi16 with a genetic distance of 0.5cM. As LrBi16 was mapped near the Lr14a locus, 809 F2 plants from the Bimai 16/RL6013 (Lr14a) cross were inoculated with the Pt pathotype FHNQ to test the allelism of Lr14a and LrBi16. All of the F2 plants were resistant to FHNQ (IT between; and 2), suggesting that Lr14a and LrBi16 are allelic.

Differential analysis of gene related to hard bunch phenomena in oil palm (Elaeis guineensis Jacq) fruits

Identification of differentially expressed genes can be done by cDNA-AFLP analysis. Hard bunch phenomena are not widely studied. The aim of this research was to identify and characterize regions specific to the gene coding sequences involved in the hard bunch phenomena in oil palm fruits. RNA was isolated from three types of ripe oil palm fruits including normal, black and hard bunch fruits. cDNAs were amplified using 16 AFLP primer pairs combinations. The result of a BLAST comparison showed that some of the resulting transcripts have sequence similarity with the existing database sequences, such as a WRKY transcription factor, peroxidase, actin depolymerising factor and glutamine synthetase allegedly associated with hard bunch phenomenon induced by drought stress. However, some transcripts could not be classified since they did not exhibit significant similarity to any existing database sequences. This is might be the transcripts were less conserve region and or 5’ or 3’ UTR region.

Genetic Variability of Spined Soldier Bugs (Hemiptera: Pentatomidae) Sampled from Distinct Field Sites and Laboratory Colonies in the United States

Abstract The spined soldier bug, Podisus maculiventris (Say), is an important biological control agent of agricultural and forest pests; and it preys on eggs and larvae of lepidopteran and coleopteran species. Genetic variability among field samples collected from Michigan, Mississippi, Missouri, Florida and established laboratory colonies was examined using Amplified Fragment Length Polymorphism-Polymerase Chain Reaction (AFLP-PCR). Four AFLP primer pairs generated a total of 340 molecular markers for evaluation. Results from Analysis of Molecular Variance showed that the majority of the genetic variation occurred within populations (individuals from each sample site). Nei's method indicated reduced genetic diversity in laboratory populations compared to field populations. No major differences or deficiencies were apparent among the field samples from different areas or among the laboratory reared samples. We conclude that field populations are panmictic and laboratory reared spined soldier bug could be ...

Identification of AFLP and SSR markers linked with the male fertility restorer gene of CMS 06J45 in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis)

AbstractIn this study, AFLP and SSR techniques were combined with the bulk segregant analysis (BSA) method to map the restorer gene BrRfp using an F2‐segregating population comprising 258 individuals developed by crossing the polima (pol)‐like cytoplasmic male sterility (CMS) line 06J45 and the restorer line 01S325 of heading Chinese cabbage. A survey of 2048 AFLP primer pairs identified 21 polymorphic fragments, approximately half of which exhibited high similarity with the A09 chromosome sequence of Brassica rapa in the Brassica database (BRAD). Based on the genome sequence, three specific AFLP fragments linked with BrRfp were successfully converted into sequence‐characterized amplified region (SCAR) markers, named SC1233, SC2673 and SC2141. Subsequently, 178 pairs of SSR primers were redesigned for further screening, with five producing polymorphic amplification patterns. Linkage analysis showed that these markers were distributed along both sides of the BrRfp gene, with two markers, SSR03 and SSR2528, co‐segregating with the BrRfp locus in the F2 population. These results may be valuable for marker‐assisted selection and map‐based cloning in heading Chinese cabbage.

Genetic Diversity of GIFT Tilapia Populations by AFLP Analysis

The experiment was conducted to assess the genetic diversity of genetically improved farmed tilapia (GIFT) in order to evaluate and preserve this strain as a germplasm resource. The experiment study focused on the genetic diversity of the newly bred F16 population of GIFT tilapia obtained from Guanghui Farm Limited Company, Huazhou (Guangdong, China) was analyzed using AFLP. 187 bands were detected with 5 pairs of AFLP primers (E-AGG/M-CTT, E-AGG/M-CTG, E-AAC/M-CAG, E-ACA/M-CTG, E-ACA/M-CAG) based on 27 individuals, and among them 163 (87.17%) were polymorphic with an average of 32.6 bands for per AFLP primer. Average Nei’s gene diversity was 0.288,6, average Shannon’s information index was 0.433,9. These results showed that the experiment group deposit had rich genetic diversity and maintained a high genetic heterozygosity, had further breeding and development value.

Analyses of genetic diversity and relationships in four Calanthe taxa native to Korea using AFLP markers

About 171 Calanthe species have been reported worldwide. However, only four species and two natural hybrids are known to grow naturally in South Korea. Classification studies of Calanthe orchids using molecular markers have been relatively limited. Therefore, the objectives of this study are to analyze the genetic diversity and relationships of four Calanthe taxa (101 accessions), including C. sieboldii (13 accessions), C. discolor (33), C. × bicolor (54), and C. aristulifera (1), native to South Korea and to identify the potential of each primer combination to discriminate each Calanthe accession using an AFLP technique. Thirty-two AFLP primer pairs produced a total of 2,764 bands, with an average of 86.4 bands per primer pair. Among all bands, 42.3% (1,354 bands), 51.6% (1,652), and 70.0% (2,240) were polymorphic in C. sieboldii, C. discolor, and C. × bicolor, respectively. Calanthe aristulifera was the most distant of the Calanthe taxa, and C. × bicolor, a natural hybrid of C. discolor × C. sieboldii, was more closely related to C. discolor (0.015 of genetic distance) than to C. sieboldii (0.022). Each Calanthe taxon with multiple accessions was divided into two or three groups. Comparisons of gene diversity, polymorphic information content, effective multiplex ratio, marker index, and resolving power proved that resolving power had the best discrimination potential for the 101 Calanthe accessions. These results will help to identify diverse accessions and to develop a breeding program of Calanthe orchids.

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.

Annotation of Differentially Expressed Genes in the Somatic Embryogenesis of Musa and Their Location in the Banana Genome

Analysis of cDNA-AFLP was used to study the genes expressed in zygotic and somatic embryogenesis of Musa acuminata Colla ssp. malaccensis, and a comparison was made between their differential transcribed fragments (TDFs) and the sequenced genome of the double haploid- (DH-) Pahang of the malaccensis subspecies that is available in the network. A total of 253 transcript-derived fragments (TDFs) were detected with apparent size of 100–4000 bp using 5 pairs of AFLP primers, of which 21 were differentially expressed during the different stages of banana embryogenesis; 15 of the sequences have matched DH-Pahang chromosomes, with 7 of them being homologous to gene sequences encoding either known or putative protein domains of higher plants. Four TDF sequences were located in all Musa chromosomes, while the rest were located in one or two chromosomes. Their putative individual function is briefly reviewed based on published information, and the potential roles of these genes in embryo development are discussed. Thus the availability of the genome of Musa and the information of TDFs sequences presented here opens new possibilities for an in-depth study of the molecular and biochemical research of zygotic and somatic embryogenesis of Musa.

DNA methylation and genetic study of interspecific hybridization in Jatropha curcas L.

Genetic relationship among Jatropha curcas L., J. gossypifolia L., J. integerrima Jacq ., J. podagrica Hook., J. multifida L. and Ricinus communis L. was studied using 10 AFLP primer pairs. A total of 564 DNA bands were generated and used for cluster analysis. Using UPGMA method, R. communis was clearly separated from Jatropha spp, as well as separated the Jatropha spp. into two groups. The first group comprised of J. curcas , J. integerrima and J. podagrica , whereas the second group consisted of J. multifida and J. gossypifolia . The interspecific hybridization was carried out between J. curcas and other Jatropha species. The results showed that cross between J. curcas and J. integerrima was the most successful. However, some hybrids were also obtained from J. curcas x J. podagrica and J. curcas x J. multifida . The observed ratio of female and male flowers of hybrids from J. curcas and J. integerrima were 1:9.1 to 1:14.9 which fall between two parents. Percentage of methylation in all hybrid derived from J. curcas x J. integerrima was lower than that of the parents. Principal component analysis of methylation fingerprints revealed that the pattern of DNA methylation in all hybrids from J. curcas x J. integerrima was more similar to J. curcas than J. integerrima. Meiotic cells of the hybrids from J. curcas x J. integerrima, J. curcas x J. podagrica and J. curcas x J. multifida were also studied. Majority of the cells investigated were normal. However, some abnormal tetrads were observed in some cells of hybrids.

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Lack of genetic diversity of a critically endangered important medicinal plant Chlorophytum borivilianum in Central India revealed by AFLP markers

Chlorophytum borivilianum is a traditional medicinal plant distributed throughout the tropics and subtropics. In the present investigation, AFLP analysis was used to assess the genetic similarity among 34 accessions. Nine primer sets of AFLP amplified 612 fragments, of which 246 fragments were found to be polymorphic. The average number of polymorphic bands per AFLP primer pair was 27.33. The amplified fragments ranged from 50 base pairs to 600 base pairs. Significant correlation was observed between total number of amplified fragments and polymorphic bands (p > 0.05) per primers. Cluster analysis based on AFLP data revealed limited genetic variation within the thirty four accessions collected from various parts of Central Indian forests.

AFLP analysis of genetic diversity of Evodia rutaecarpa

To study the genetic background of Evodia rutaecarpa by AFLP, and analyze the genetic diversity of E. rutaecarpa from different areas. E. rutaecarpa genomic DNA was extracted. The AFLP reaction system was established and AFLP primer pairs were chosen for the analysis. Forty-six individuals of E. rutaecarpa which from five provinces were analyzed by AFLP. The NTSYS-pc 2.1 software was used for cluster analysis. Six out of the original 72 pairs of primers were optimized for the study; AFLP analysis revealed the similarity coefficient of 0.53, the samples of E. rutaecarpa var. officinalis from Zhejiang province was separated from other accessions; E. rutaecarpa var. officinalis also showed more pronounced genetic variation than the E. rutaecarpa, and strong geo-related relevance. Variance of genetic background of E. rutaecarpa are large, AFLP analysis method can obviously identify different varieties of E. rutaecarpa, and can detect the genetic characteristics of inter-regional differences.

Genetic structure and diversity of India hybrid tea

The most important evolutionary event in the success of commercial tea cultivation outside China in ~30 countries came about by the origin of India hybrid tea in India, derived from the extensive spontaneous hybridization that took place between the Assam type tea growing in the forest regions of Assam, North-East India and China type tea introduced from China in ~1875 to many regions of North-East India. The release of an enormous pool of vigorous and highly variable plants of India hybrid tea in North-East India was a significant step forward for the origin and evolution of tea as a highly successful crop plant. The 1,644 accessions and clones of India hybrid tea, representatives of known 15 morphotypes, were screened by 412 AFLP markers amplified by 7 AFLP primer pair combinations. All the 412 genetic loci were polymorphic across the 1,644 accessions and clones. The analysis was done with distance (PCoA and NJ) methods, and the STRUCTURE (Bayesian) model. Both PCoA and NJ analysis clustered 1,644 tea accessions and clones into six major groups with one group in each, constituted mostly by China hybrid, Assam China hybrid and Assam hybrid morphotypes, of distinct genetic identity. No group was exclusive for any particular morphotype. The accessions and clones belonging to morphotypes, Assam type, Assam hybrid, China hybrid and China Cambod were distributed in all the groups. It is the Assam type/Assam hybrid morphotypes which exhibit much broader genetic variability than in China type/China hybrid/Cambod type/Cambod hybrid morphotypes. The STRUCTURE analysis inferred 16 populations (K = 16), for which the greatest values of probability were obtained. Nine of the 16 clusters were constituted by the tea accessions and clones of ‘pure’ ancestry. The remaining clusters were of ‘mixed’ ancestry. This analysis provides evidence that the accessions and clones of the same morphotype are not always of same genetic ancestry structure. The tea accessions and clones obtained from outside North-East India shared the same groups (distance method) and clusters (STRUCTURE model) which were constituted by North-East India accessions. The present study also demonstrates very narrow genetic diversity in the commercial tea clones vis-a-vis the profound genetic diversity existing in the tea accessions. These clones were distributed in hardly two of the six groups in NJ tree. The identified 105 core accessions and clones, capturing 98% diversity, have their origin from almost all groups/subgroups of NJ tree.