Amplified Fragment Length Polymorphism Primer Combinations Research Articles

AFLP-based assessment of genetic variation in certain Indian elite cultivars of Cymbopogon species

Cymbopogon, one of the major aromatic genera of Poaceae family, is mainly cultivated for its essential oils that hold promising medicinal and commercial value. In India, several improved cultivars of Cymbopogon species are developed for commercial cultivation and conceded by means of agronomic and chemotypic traits. Information on genetic variability in these commercial cultivars is still limited which poses a problem in further improvement of oil grasses. The present study aimed to investigate the genetic variation among certain improved Indian cultivars of three commercially important Cymbopogon sp. i.e., C. flexuosus, C. winterianus and C. martinii using amplified fragment length polymorphism (AFLP) markers. A total of 94 robust loci were amplified using 8 AFLP primer combinations. Among the total amplified fragments, 72 were polymorphic which showed 76.59% polymorphism across all the germplasm. Polymorphic information content (PIC) and marker index (MI) values showed significant positive correlation (r2 =0.936, p < 0.005) in determining the discriminatory power of the AFLP primer combinations. A higher effective multiplex ratio (EMR) and MI values were recorded for the primer combinations that generated higher polymorphism across the genotypes. To obtain the genetic information at the intra- and inter species level, genetic diversity indices were calculated. Genetic heterogeneity was noticed in the order C. martinii>C. flexuosus>C. winterianus. UPGMA-phenogram and principal coordinate analysis (PCA) separated all the cultivars as per the chemotaxonomic series with a few exceptions. Molecular diversity explained and diagnostic fragments developed through AFLP markers in this study could provide a detailed cataloguing of Cymbopogon cultivars for genetic conservation purpose and also useful for exploration and improvement of diverse set of germplasm.

High Quantitative Trait Variability in Faba Bean Mutagenized Population for High-yielding Breeding Program in Saudi Arabia

Background: The narrow genetic base and environmental stresses are behind the low rate of faba bean yield in the past two decades. Drought stress is one of the most destructive abiotic stresses. Using induced mutagenesis on locally adapted landrace cultivar is proposed to cope with this problem. Methods: This study was conducted on faba bean landrace cultivar of Saudi Arabia, namely Hassawi 2, treated by 25 and 50 Gray gamma radiation. The genetic diversity assessment of M2 mutant populations was based on seven quantitative traits and nine Amplified Fragment Length Polymorphism (AFLP) primer combinations. Result: A total of 3419 M2 seeds were planted, of which 2782 (81.4%) seeds germinated and 2658 plants survived. A 5 to a 10-fold range of quantitative traits studied among mutant plants compared to control plants showed high variability. The number of pods per plant and seeds per plant was a valid selection criterion for a high-yielding faba bean breeding program. Nine AFLP primer combinations generated 1079 polymorphic alleles from 88 samples that comprised mutant and control plants. Shannon index (I) and expected heterozygosity (He) were 0.337 and 0.206, respectively. The AFLP results validated high variability in M2 populations. These findings will assist faba bean breeders in developing high-yielding cultivars with drought stress tolerance.

AFLP markers based genetic diversity and population structure analysis of Kadaknath: an indigenous black meat poultry breed of India

The current study is the first worldwide to assess the genetic diversity of Kadaknath poultry using amplified fragment length polymorphism (AFLP) markers. Out of total 96 accessions, four were outliers and 92 were Kadaknath accessions of which 30 were males, 62 were females. Of these, 74 were jet black, 7 penciled and 11 were golden feather color type of Kadaknath. High level of polymorphism (23.94%) was observed in 387 loci amplified using six AFLP primer combinations. The Jaccard’s similarity coefficient ranged from 0.211 to 0.754 with an average dissimilarity of 0.517. Based on the neighbor-joining method of clustering, all accessions were clustered into seven major clusters which were not consistent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, resolving power and marker index were 15.16, 0.38, 9.87 and 5.85 respectively. Further, the high log-likelihood score was produced when the number of populations (K) was set at 7 while carrying out the population STRUCTURE analysis, which was also congruent with clustering analysis based on genetic diversity. The extent of genetic diversity detected in this study could be used for germplasm selection and developing conservation strategies of pure breed of Kadaknath.

Assessment of phylogenetic relationship among twenty Curcuma species in Thailand using amplified fragment length polymorphism marker.

Plants in the genus Curcuma are a rhizomatous perennial herb which is widely distributed in Thailand. It has long been known for their uses as folk medicines, foods, spices, and cosmetics. However, the identification of plants in the genus Curcuma is very difficult due to morphological similarity in the early flowering stage. Recently, the molecular technique is one of the reliable and powerful tools for plant identification. In this study, the genetic relationship among twenty Curcuma species from Thailand was accessed by the amplified fragment length polymorphism (AFLP) method. AFLP fingerprint showed 98.54% highly polymorphisms with the number of bands (617 bands) ranging between 48 and 80 bands. The dendrogram generated from the unweighted pair group method of the arithmetic average could separate these Curcuma species into three major clusters. Cluster I can be subdivided into IA, which composed of Curcuma parviflora, Curcuma sparganiifolia, Curcuma alismatifolia, Curcuma larsenii, Curcuma Gracillima, and Curcuma rhabdota with similarity index (SI) 0.7926–0.9358 and IB composed of Curcuma petiolata and Curcuma rubrobracteata with the SI 0.9240. Cluster II can be subdivided into IIA being composed of Curcuma longa, Curcuma Zedoaria, and Curcuma aromatica with the SI 0.8989–0.9071, whereas Cluster IIB was composed of Curcuma leucorrhiza, Curcuma aeruginosa, Curcuma comosa, Curcuma mangga, Curcuma angustifolia, Curcuma amada, Curcuma sessilis, and Curcuma albicoma with the SI 0.8236–0.9500. Cluster III belongs to Curcuma singularis and Alpinia galanga (outgroup plant), which clearly separated into different clusters from twenty Curcuma species. In summary, the ten successful AFLP primer combinations could be used to determine the genetic relationship among closely related twenty Curcuma species in Thailand.

Genetic Diversity and Population Structure Analysis of Sand Pear (Pyrus pyrifolia) ‘Nakai’ Varieties Using SSR and AFLP Markers

In this study, the technologies of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers were used to analyze the genetic diversity of 30 sand pear (Pyrus pyrifolia) ‘Nakai’ varieties. Ten pairs of SSR polymorphic primers were selected to amplify P. pyrifolia ‘Nakai’ varieties. A total of 90 alleles were detected. The polymorphism information content index was between 0.5578 and 0.8423, with an average of 0.7585. The selected 10 pairs of AFLP primer combinations were used to amplify the analyzed pear varieties, and 1,046 polymorphic loci were detected. The average amplification results of each primer combination detected 105 bands with an average polymorphism percentage of 86.46%. The combined data of SSR and AFLP analysis showed that the analyzed P. pyrifolia ‘Nakai’ varieties were characterized by extremely rich genetic diversity and were highly representative. According to the results of SSR, AFLP, and SSR+AFLP cluster analysis, the analyzed P. pyrifolia ‘Nakai’ varieties can be categorized into three clusters. The results of genetic structure showed that the hybridization between these P. pyrifolia ‘Nakai’ varieties resulted in the heterozygosity of genotypes. In addition, we found that ‘Nijisseik’, ‘Ejima’, and ‘Fuli’ are good parent resources among the pear varieties through observing the genetic background of the analyzed pear varieties. This study reveals the genetic diversity levels of P. pyrifolia ‘Nakai’ varieties at the molecular level, which was important in molecular identification and protection of pear germplasm resources, as well as pear variety breeding and genetic improvement.

English

Among the biological constraints facing maize production in Tanzania is a severe occurrence of maize lethal necrosis disease (MLN) raising an urgent need for application of new approaches. A pool of 22 maize genotypes with promising resistance and susceptibility to MLN infection were evaluated by Amplified fragment length polymorphism (AFLP) DNA fingerprinting analysis to detect genetic variation in the selected lines. Eleven AFLP primer combinations were screened and resulted in the identification of 95 polymorphic AFLP allelic fragments. Genetic similarities among the selected Tanzanian maize landraces and other maize lines were estimated by Unweighted Pair Group of Arithmetic Mean (UPGMA) and genotypes were clustered in three primary groups according to their reaction to MLN disease. Promising resistant and tolerant genotypes were grouped in cluster I and susceptible genotypes in clusters II and III. Landraces were grouped according to agro-ecological locations where they were collected. Unambiguous polymorphic AFLP fragments were eluted, purified and sequenced. Sequencing and nucleotide alignment on Basic Local Alignment Search Tool (BLAST) analysis showed similarities of fragments consistent with transcripts involved in disease resistance and stress responses. Further studies will explore the potential application of the identified AFLP markers and their significant association to MLN disease resistance genes in maize. Key words: Zea mays, AFLP, maize lethal necrosis disease, Tanzania.

Analysis of genetic diversity evaluation of Lysiphyllum strychnifolium (Craib) A. Schmitz in Thailand using amplified fragment length polymorphism markers

Lysiphyllum strychnifolium (Craib) A. Schmitz, a Leguminosae-Caesalpiniodeae species, is colloquially known in Thai as Ya Nang Daeng. In Thai traditional medicine, the leaves, stems and roots have been used to relieve fever and alcohol toxication. The stem has also been used for anti-HIV-1 integrase, anti-allergy and anti-cancer treatment. Confusion over herbal drugs has arisen from the homonymity and morphological characteristics, which present many similarities within its family. Thus, germplasm collection and genetic diversity analysis are prerequisites for a breeding program. In this study, the amplified fragment length polymorphism (AFLP) marker was used to identify and elucidate the phylogenetic relationships among 98 accessions of Ya Nang Daeng throughout Thailand. Thirteen AFLP primer combinations generated 379 bands, of which 359 were polymorphic. The value of the similarity coefficient varied from 0.52 to 0.93, with a mean of 0.73. A phylogenetic tree was constructed using the unweighted major clusters at a cut-off genetic mean (UPGMA) clustering method. The phylogenetic tree derived from the AFLP data showed that the Ya Nang Daeng accessions could be divided into two clusters. Cluster 1 could be further classified into five subgroups, while a similarity coefficient of 0.23 could be used to separate an outgroup from Ya Nang Daeng. The result of principal coordinate analysis and morphological grouping corresponded to the UPGMA clustering. This study showed that the AFLP technique is a useful tool for estimating DNA polymorphism of the genetic diversity and differentiation of related plants. This genetic information will provide useful information for a breeding program in the future.

Assessment of genetic diversity of Smallanthus sonchifolius (Poepp. &amp; Endl.) h. Robinson landraces by using AFLP markers

AFLP (Amplified Fragment Length Polymorphism) analysis was carried out on Smallanthus sonchifolius to increase the knowledge on its genetic diversity. It is an ethnomedical and edible plant native of Peru and cultivated in many other countries. Thirteen landraces were analyzed by selected AFLP primer combinations generating a number of 185 fragments, of which 180 were polymorphic (97.00% of polymorphism). The mean value of fragments per primer combination was 37, but MseI (M)-CAG/EcoRI (E)-ACT primer combination reported the highest number with 63 amplicons, instead only 27 were revealed by M-CAG/E-ACC. The marker attributes such as resolving power (RP), marker index (MI) and polymorphism information content (PIC) were determined. RP values varied from 11.54 (M-CAG/E-ACC) to 27.54 (M-CAG/E-ACT), PIC ranged from 0.25 (M-CAG/E-AGC) to 0.28 (M-CAG/E-ACA), whereas MI values were found to be in the range from 6.18 (M-CAG/E-ACC) to 15.95 (M-CAG/E-ACT). Cluster analysis and PCA were evaluated for determining relationships among yacon landraces. We concluded that AFLP markers showed a highest efficiency in estimating genetic diversity in yacon despite to previous paper in which 3 times lower samples have been analyzed.

IDENTIFICATION OF A SCAR MARKER LINKED TO A SHATTERING RESISTANCE TRAIT IN SESAME

Sesame (Sesamum indicum L.) is one of the most important oil crops in temperate and tropical regions and is grown worldwide over an area of 5179 (hg ha-1 ) to produce 5.469.024 tonnes of seed. Capsule shattering before or during harvest can cause yield losses of greater than 50%. The objectives of the present study were to evaluate the inheritance of resistance to capsule shattering in the F2 derived from a cross between Cplus1, a sesame line with shattering-resistant capsules (Sh1Sh1Sh2Sh2), and KUAOX25, a line with shatteringsusceptible capsules (sh1sh1sh2sh2- ); and use bulked segregant analysis and Amplified Fragment Length Polymorphisms (AFLPs) to identify Sequence Characterized Amplified Region (SCAR) markers associated with shattering resistance. After screening 192 AFLP primer combinations, nine polymorphic bands were identified, and one of these AFLPs was developed into a Si-SR-32-19 SCAR that could distinguish between shattering-susceptible and shattering-resistant phenotypes.

Molecular genetic diversity and mating system in sacha inchi progenies1

ABSTRACT Sacha inchi (Plukenetia volubilis L.) is a species with nutraceutical benefits traditionally consumed by Amazonic indigenous and urban communities. Studies on the genetic diversity and mating system are required to preserve and make the best use of the genetic resources for this species. This study aimed to estimate the genetic diversity and mating system parameters of sacha inchi progenies using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 360 progenies from 30 accessions of sacha inchi were analyzed using three AFLP primers combinations. The percentage variation between and within families and the crossing rate, among other parameters, were estimated. The AFLP markers were efficient in genetically differentiating progenies, revealing 251 (98.82 %) polymorphic fragments. The analysis of molecular variance showed that the strongest variation occurs between progenies (57.16 %). However, the genetic differentiation within progenies was considerable (42.84 %), and could be exploited in breeding programs. The estimated population outcrossing rate was high (0.957), indicating it is a predominantly allogamous species. On the other hand, 33.7 % of the crosses occurred between related individuals. The estimate for biparental crosses revealed that the progenies consisted mainly of half-siblings (66.9 %) and full-siblings (28.8 %). For purposes of breeding and ex situ genetic conservation, sacha inchi seeds should be collected from a large number of parent plants.

Genetic variability in Indian populations of banana corm weevil [Cosmopolites sordidus (Coleoptera: Curculionidae)] assessed by RAPDs and AFLPs

AbstractCosmopolites sordidus(Germar), commonly known as banana corm weevil, is an important economic pest in Asia that can cause severe yield loss depending upon the stage at which infestation occurs. In spite of its economic importance, little is known about the population structure of this pest in India. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to characterize the population genetic structure ofC. sordiduscollected from five hot spot locations in India. Nineteen RAPD primers and five selective AFLP primer combinations generated 147 and 304 amplification products, respectively. UPGMA dendrograms generated with both marker systems failed to reveal populations clustered based on geographic distance, which was confirmed by the Mantel test, which did not show a strong correlation between genetic distance and geographic distance. Values of indices of genetic identity showed that the populations were closely related. Though the gene flow estimate (Nm) between the populations was 0.469, suggesting restricted gene flow, the populations are not genetically distinct. These observations suggest that the range expansion of this banana pest in India has taken place through transport of infested corms and plant material, resulting in genetically close populations that are geographically distinct. These results provide important information on the population structure of this pest in India, which will aid in designing suitable strategies for its control and management, especially with respect to insecticide resistance.

Study on the genetic variability of the hatchery-released and wild populations of Chinese white shrimp Fenneropenaeus chinensis in the Yellow Sea and Bohai Sea

In relation to the stock enhancement program for Chinese white shrimp Fenneropenaeus chinensis, hatchery-released juveniles and wild samples in the Yellow Sea and Bohai Sea were genotyped using amplified fragment length polymorphism (AFLP) markers to investigate the levels of genetic variation among these populations. Five AFLP primer combinations generated a total of 757 bands across the 268 individuals in nine hatchery-released populations and three wild populations. All 757 bands were polymorphic. High polymorphism at AFLP markers was found within both hatchery-released and wild populations. The percentage of polymorphic loci for populations ranged from 87.22 to 98.60%, while the Nei’s genetic diversity ranged from 0.1822 to 0.2728. Compared with wild populations, the nine hatchery-released populations showed significant genetic changes based on F ST values. All populations were divided into two distinct groups by principal coordinate analysis (PcoA) analysis. Three wild populations (Dalian, Kengli, Middle Yellow Sea) with hatchery-released populations from Rongcheng, Panjin, and Dandong clustered as one group; the rest of hatchery populations formed another group. Interestingly, no obvious geographic cluster was found in the unweighted pair group method with arithmetic mean tree and PcoA. We recommend monitoring the genetic variability of selected hatchery populations to enhance the conservation of natural Chinese white shrimp F. chinensis resources.

Genetic Diversity and Relationships among Sugarcane (Saccharum sp.) from Thailand Revealed by RAPD and AFLP Markers

Objective: The objective of the present research was to evaluate the genetic diversity and relationships of sugarcane ( Saccharum sp.) that collected from the sugarcane germplasm collection, Thailand. Methods: Genetic diversity of sugarcane was detected by DNA sequencing, Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) markers. Findings: The trnL- trnF region of the chloroplast genome was amplified for 26 cultivars with C and F primers that the fragment was approximately 950 base pairs (bp). The taxonomic status and relationships of these sequences are not resolved. RAPD marker was used to study genetic variation and relationships among 56 sugarcane varieties and their hybrids. Ninety-six RAPD primers were screened and nine primers of them produced reproducible and recordable bands were used in analysis. The eighty-eight polymorphic bands (96.70%) were detected and genetic similarity was 0.657. The best five AFLP primer combinations were selected and generated 187 polymorphic bands (80.26%). Comparing the results from the RAPD and AFLP markers in 19 sugarcane cultivars, the genetic similarity ranging from 0.582 to 0.927, with the average of 0.756 for AFLP and ranging from 0.449 to 0.865, with the average of 0.657 for RAPD that demonstrating a low level of genetic diversity. For dendrogram analysis, AFLP marker showed itself to be more efficient at discriminating sugarcane cultivars. However, the genetic relationship of the samples slightly correlated with sucrose content. Application: RAPD and AFLP markers can be used to help plant breeder to select cultivars for future sugarcane improvement programs.

Association analysis of biotic and abiotic stresses resistance in chickpea (Cicer spp.) using AFLP markers

ABSTRACTChickpea suffers from different biotic and abiotic stresses, which has led to considerable decreases in seed yield. Since the economic value of a cultivar is determined by its phenotypic characteristics, good knowledge of the genetic structure and identification of genomic loci associated with desired traits will facilitate crop breeding. Amplified fragment length polymorphism (AFLP) markers associated with different agro-morphological characteristics, cold and drought tolerance as well as Ascochyta blight resistance were identified in chickpea by using 44 genotypes comprising cultigens, landraces, internationally developed improved lines and wild relatives, evaluated in a randomized complete block design with three replications at the Urmia rainfed research station. Using six AFLP primer combinations, 64 clear and reproducible markers were developed. The polymorphism information content values calculated for each primer pair ranged from 0.155 (EcoR1-ACC/Mse1-CAG) to 0.270 (EcoR1-ACC/ Mse1-CTG) with an average of 0.237. Analysis of molecular variance (AMOVA) revealed that 90% of the total variance was due to differences within populations and 10% due to differences among populations. Using a general linear model and applying multiple testing corrections, 24 AFLP markers associated with genes controlling the studied traits were identified. Some identified markers were associated with more than one trait. The identified markers could be of interest in marker-assisted selection in chickpea breeding programmes.

Estimation of Outcrossing Rates in Biodiesel Species Pongamia pinnata Based on AFLP and Microsatellite Markers

Outcrossing rates in biodiesel species Pongamia pinnata were estimated using amplified fragment length polymorphism (AFLP) and microsatellite markers. Five AFLP primer combinations and eight pairs of microsatellite primers were used for fingerprinting of 55 open pollinated progenies derived from five mother trees. The multilocus out-crossing rate was quite high with AFLP (0.917; SD = 0.103) and comparatively low with microsatellite markers (0.748; SD = 0.127). The multilocus out-crossing rate was higher than single locus out-crossing rate in case of both marker systems (tm − ts = 0.203; SD = 0.090) which implies that biparental inbreeding occurred at significant levels. The estimated F was higher than the expected which also indicated towards high inbreeding in the progeny population analyzed. This is the first study on estimation of outcrossing rates using any kind of molecular marker systems in Pongamia. We expect an increasing use of such high throughput PCR-based technologies in mating-system studies in various other tree species.

Molecular genetic diversity and association mapping of nut and kernel traits in Slovenian hazelnut (Corylus avellana) germplasm

European hazelnut (Corylus avellana L.), cultivated in several areas of the world including Europe, Anatolia, and the USA, is an economically important nut crop due to its high mineral, oleic acid, amino acid, and phenolic compound content and pleasant flavor. This study examined molecular genetic diversity and population structure of 54 wild accessions and 48 cultivars from the Slovenian national hazelnut collection using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Eleven AFLP primer combinations and 49 SSR markers yielded 532 and 504 polymorphic fragments, respectively. As expected for a wind-pollinated, self-incompatible species, levels of genetic diversity were high with cultivars and wild accessions having mean dissimilarity values of 0.50 and 0.60, respectively. In general, cultivars and wild accessions clustered separately in dendrogram, principal coordinate, and population structure analyses with regional clustering of the wild material. The accessions were also characterized for ten nut and seven kernel traits and some wild accessions were shown to have breeding potential. Morphological principal component analysis showed distinct clustering of cultivars and wild accessions. An association mapping panel composed of 64 hazelnut cultivars and wild accessions had considerable variation for the nut and kernel quality traits. Morphological and molecular data were associated to identify markers controlling the traits. In all, 49 SSR markers were significantly associated with nut and kernel traits [P < 0.0001 and LD value (r 2) = 0.15–0.50]. This work is the first use of association mapping in hazelnut and has identified molecular markers associated with important quality parameters in this important nut crop.

RETRACTED ARTICLE: Genetic Structure and Diversity Analysis Revealed by AFLP Markers on Different Glycyrrhiza glabra L. an Endangered Medicinal Species from South of Iran and Implications for Conservation.

Glycyrrhiza glabra is an endangered and national-protected medicinal plant species distributed in semi-arid and arid areas of South of Iran. This study addresses the genetic diversity and relationship between populations in different habitats by amplified fragment length polymorphism (AFLP). The plant materials consisted of 90 individuals from nine different populating areas of Dezful, Ramhormoz, Ahvaz, Abadan, Khorramshahr, Behbahan, Haft-tapeh, Andimeshk, and Shushtar. Twenty-three AFLP primer combinations generated a total of 1019 bands with 94.80 % polymorphism. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in wild populations of G. glabra were rich. The number of polymorphic fragments per primer combination detected ranged from 18 to 65 bands with an average of 41.95 bands. Average polymorphic information content (PIC) was 0.81 in overall primer combinations. M-GTC+P-AGC primer combination showed the highest PIC (0.94) which can be a good candidate primer combination to verify genetic diversity in G. glabra. The UPGMA and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of three groups. The study showed that genetic variation and population structure are determined among the accessions of G. glabra collected from different locations. High level of genetic variation in both intra- and inter-species was detected. Conservational efforts have to be strengthened for all populations of the plant species in different habitats.

Genetic diversity of the African poplar (Populus ilicifolia) populations in Kenya

We evaluated the genetic diversity of the African poplar (Populus ilicifolia) populations found in Kenya compared with reference samples of five poplar species from North America and one species introduced in Kenya from India (KEFRI-Kenya). Amplified fragment length polymorphism (AFLP) was used with the objective of providing important information for breeding and in situ/ex situ conservation of this species. Samples collected from three locations along the species’ natural range (Athi, Ewaso Nyiro, and Tana rivers) were compared with four samples of locally planted Populus deltoides stand introduced from India and ten reference samples from North America. Six AFLP primer combinations produced 521 clear bands for analysis. The percentage polymorphic loci were lowest in Tana (20.4 %) and highest in Athi (40.6 %). The average heterozygosity across the studied populations was between 0.07 and 0.3. AMOVA revealed more genetic variation partitioning within population (87 %; P < 0.01) than among populations (13 %; P < 0.01) suggesting significant genetic variation between populations. Further, UPGMA delineation showed two clusters of the Tana, Athi, and Ewaso Nyiro populations clustered together compared to the North America and India/KEFRI reference samples. Moreover, the study showed that the Athi population is more diverse than those of Tana and Ewaso Nyiro and may be important for conservation, domestication, and improvement studies. The genetic differentiation (FST = 0.134) among Kenyan P. ilicifolia populations suggests limited possibility of gene flow between these populations.

The power of microsatellite markers and AFLPs in revealing the genetic diversity of Hashemi aromatic rice from Iran

Hashemi, a popular aromatic rice among Iranians, is famous for its fragrance and taste. Such features are major reasons for its higher price compared to non-aromatic varieties available in Iran. Therefore, the knowledge of genetic diversity of this profitable crop is a fundamental ineterst for plant breeders in future breeding programs. In the present research, genetic diversity among 35 genotypes of Hashemi aromatic rice (Oryza sativa L.) from Guilan and Mazandaran provinces of Iran was estimated using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Out of 21 SSR and 12 EcoRI-MseI AFLP marker combinations, only 16 SSRs and 10 AFLPs exhibited polymorphic patterns while others were monomorphic. The 10 AFLP primer combinations produced a total of 142 of bands and 20 were polymorphic (14.08%). Moreover, 40 out of 47 bands amplified with 16 SSR markers showed polymorphism (85.1%). The average number of alleles identified by SSR primers was 2.56 alleles per locus with a range of 2 to 4. The average value of polymorphic information content (PIC) was 0.393 and 0.468 for AFLP and SSR markers, respectively. However, the genetic similarity values ranged from 0.26 to 1 for SSRs and 0.21 to 1 for AFLPs. Later, a unweighted pair group method with arithmetic mean (UPGMA) dendrogram was generated and genotypes were clustered into four groups with SSRs at similarity coefficient of 0.55 while AFLPs clustered them into six groups at similarity coefficient of 0.41. Cluster analysis revealed a narrow genetic diversity and low correlation between geographical differentiation and genetic distance within cultivars.

Identification of candidate AFLP markers for shell color of the Pacific oyster (Crassostrea gigas) under artificial selection

The shell color of the Pacific oyster (Crassostrea gigas) is a desirable trait, but only a few genetic studies on shell color have been documented. Through successive selective breeding, four shell color variants of white (W), gold (G), black (B) and purple (P) C. gigas have been developed. The amplified fragment length polymorphism (AFLP) technique was used to scan the genomes of the four variants with different shell colors and one wild population (C) to identify candidate markers for shell polymorphism. Fifteen AFLP primer combinations were used, 1079 loci were scored as polymorphic loci, and the percentage of polymorphic bands was 95.5%. In the gold, white, black, purple and wild populations, the percentages of polymorphic loci were estimated to be 90.5% (G), 90.0% (W), 91.1% (B), 95.3% (P) and 93.2% (C); the expected heterozygosity values were 0.3115 (G), 0.3044 (W), 0.3102 (B), 0.3285 (P) and 0.3105 (C). The white shell variant was observed to have slightly lower genetic diversity than others, with a FST value of 0.1483. These results indicated that the four different shell color variants had high genetic diversity and that the genetic differentiation of populations mostly results from genetic diversity of individuals within populations. Furthermore, 11 outlier loci were considered candidate markers for shell color. This work provides new insights on relationships among color variants of C. gigas.