Pairwise Similarity Coefficient Research Articles

Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d’Orbigny) in Con Dao and Phu Quoc islands, Vietnam

BackgroundBigfin squid is one of the economically important seafood resources in Vietnam’s fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box–derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. ResultsCon Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. ConclusionsFor the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.

Stevia rebaudiana germplasm characterization using microsatellite markers and steviol glycosides quantification by HPLC

Stevia rebaudiana Bertoni, Asteraceae, is an herbaceous perennial plant native to Paraguay. This species is considered since ancient times a medicinal plant with important bioactive compounds and pharmacologic and food properties, namely diterpenes glycosides. The high natural sweetener potential stevioside and rebaudioside A produced by S. rebaudiana plants are suitable sucrose substitutes, and their obtention is influenced by environmental, phytosociological, and genetic factors. The plants’ genetic profile and sweet potential depiction are needed for suitable plant selection for improvement and deployment. Thirty-one S. rebaudiana accessions grown in the same plot where leaves samples were collected in early 2019, were genotyped using six microsatellite markers, including two steviol glycosides biosynthesis functionally involved markers. Additionally, an aqueous extract of each sample was obtained in a water bath and purified by SPE for stevioside and rebaudioside A quantification by normal phase HPLC. Stevioside and rebaudioside A contents varied between 0.53–7.36% (w w−1) and 0.37–3.60% (w w−1), respectively. Two genotypes displayed interesting ratios of rebaudioside A/stevioside (number 3 and 33). The level of genetic similarity between genotypes was tested through a pairwise similarity coefficient, and two groups of individuals had the same fingerprinting. Strong relatedness was found within genotypes, possibly due to cloning, thus, influx of new germplasm ought to be made to prevent mating between relatives, and for further selection and genetic improvement.

Genetic diversity and population structure of Iranian pistachio (Pistacia vera l.) cultivars

Iran has a rich pistachio germplasm, thereby, the diversity and number of Iranian pistachio cultivars is unique in the world. Genetic diversity is crucial for sustainable use of genetic resources and conservation. As one of the oldest nut crops in human history, pistachio nuts have a high nutritional value and are commercially important. In the present study, the genetic variation of pistachio genotypes was investigated by nuclear ISSR markers. In this study, genetic relationships among 11 cultivars was assessed by using 12 inter simple sequence repeat (ISSR) primers. The total of 53 bands of which 44 (83%) were polymorphic were amplified by the 12 primers, an average of 4.4 bands per primer. The total number of amplified fragments was between 2 to 6 and the number of polymorphic fragments ranged from two to six. The amplified allele sizes ranged from 300 to 1600 bp. Pair-wise genetic similarity coefficients varied from 0.70 to 0.95. The UPGMA dendrogram differentiated the genotypes into two major clusters. The Mantel test showed correlation between genetic and geographical distance. AMOVA revealed a significant genetic difference among cultivars and showed that 35% of total genetic variation was due to within- cultivars diversity. The present results may be used for the conservation, core collection and future breeding of the pistachio.

GENETIC DIVERSITY OF NATURALLY DISTRIBUTED Rhododendron moulmainense Hook. f. POPULATIONS IN LAM VIEN PLATEAU, VIETNAM REVEALED BY ISSR AND SCoT MARKERS

Genetic diversity and variation of three naturally distributed Rhododendron moulmainense populations in the Lam Vien Plateau of Vietnam were analyzed using ISSR and SCoT markers separately and data from the two types of markers were then combined to show the overall results. Based on combined data, the genetic diversity parameters of the Tuyen Lam population were percentage of polymorphic bands (PPB) = 28.79%; genetic heterozygosity (He) = 0.1041; Shannon index (I) = 0.1552. The corresponding parameters were PPB = 37.88%; He = 0.1434; I = 0.2131 in the Hon Nga population, and PPB = 46.21%; He = 0.1857; I = 0.2709 in the Bidoup population. At the species level in Lam Dong province, the corresponding parameters were PPB = 62.12%; He = 0.1747; I = 0.2756. The average of pairwise genetic similarity coefficients among investigated individuals of Tuyen Lam population was 0.973, of Hon Nga population was 0.911, and of Bidoup population was 0.895. The genetic differentiation and the number of migrants per generation among investigated populations were GSTS = 0.1735 and Nm = 2.3824 individuals, respectively. Genetic distance between Tuyen Lam and Hon Nga populations was 0.0399, between Tuyen Lam and Bidoup populations were 0.0621, and Bidoup and Hon Nga populations were 0.0670. Data generated by both marker types and the combined revealed similar trends of genetic diversity levels among the studied populations. The SCoT data showed higher values of genetic diversity and population gene differentiation than did the ISSR data, but the latter showed higher gene differentiation among sampled individuals in the study populations. Comparing the values of Polymorphism Information Content (PIC) for discriminatory ability; Effective Multiplex Ratio (EMR) for several revealed loci and/or efficiency of the primer-marker system; Marker Index (MI) for the efficiency of used method; and Resolving Power (Rp) between used techniques indicated that discriminatory ability, efficiency, and ability of the ISSR primer combinations were higher but using SCoT marker system was more efficient than ISSR marker system for evaluating genetic diversity.

Genetic Diversity in Egyptian Snake Melon Accessions as Revealed by Inter Simple Sequence Repeat (ISSR) Markers

Snake melon (Cucumis melo var. flexuosus) is native to the region from Egypt to Iran; therefore, local genotypes in Egypt may contain genes responsible for tolerance to biotic and abiotic stresses. However, no previous studies were done on the genetic diversity in this crop in Egypt. ISSR markers were used to examine genetic relations among 12 Egyptian snake melon accessions collected from different regions. Of the 10 markers tested, 6 produced 68 amplification products, of which, 23 were polymorphic (33.7% polymorphism). The average polymorphism information content (PIC) value was 0.68 over the 6 primers. Pairwise Jaccord's similarity coefficient ranged from 0.88 to 0.98, indicating a narrow diversity. Cluster analysis distinguished two clusters, one from Cairo, and the second represents the rest of accessions from different regions. It was shown that snake melon genotypes that were genetically close were not necessarily close in geographical distance. On a level of non-coding region using 6 ISSR primers, some differences were found among the Egyptian snake melon accessions, confirming the usefulness of the technique in detecting genetic diversity which may help in future genetic improvement programs in this underestimated crop.

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.

Study on the genetic variability and pathogenicity assessment among isolates of spot blotch causing fungi (Bipolaris sorokiniana) in wheat (Triticum aestivum L.)

Wheat is the second largest consuming crop in the world. The yield attributes are hit by many biotic as well as abiotic stress for this crop. Spot blotch which is caused by Bipolaris sorokiniana, a major disease infests into this crop. This fungus flourishes in the humid conditions and mostly affects the Indo-Gangetic plain area. So we have done this extensive research to characterize the fungus and its pathogenicity. The experiment was laid out into Randomized Block Design with three replications to screen the genotype under field conditions for spot blotch susceptibility in the Rabi season of 2016–2017 at Borlaug Institute for South Asia. The greenish grey group had a maximum frequency of 31.25 among all the isolates in the natural population. Radial growth was maximum in RAU-GTL-34 (40.66 mm) having cottony growth pattern and dull white with rings like marking. The mean pathogenicity value showed that isolates were more pathogenic on Sonalika (3.7) than Chiriya 3 (2.5). Colony color and level of exudations were also observed to be related to the level of pathogenicity and aggressiveness. Area under disease progress curve of isolates on Chirya 3 varied from 198.77 (white group) to 730.25 (black group) in both natural and polyhouse condition, while for Sonalika it varied from 458.02 (white group) to 134.83 (black group) in natural condition, whereas from 458.02 (white group) to 1374.07 (black group) in polyhouse condition. Fungus specific primer Cos A_F/R was identified for all isolates as B. sorokiniana. Two Internal transcribed spacer (ITS) primer gave a total of 22 alleles out of which twelve were monomorphic and ten were polymorphic with an average of eleven alleles per loci. The Polymorphism Information Content values varied from 0.884 to 0.915 with an average of 0.88. PCR–RFLP analysis gave a total sixty-six allele out of which thirty unique alleles and thirty-six shared alleles with an average of 7.3 alleles per loci in both the region. The Polymorphism Information Content values varied from 0.331 (ITS-2 and Hinf-I) to 0.809 (ITS-2 and Hind III). Pair-wise genetic similarity coefficients widely varied from 0.54 to 1.0 indicating similarity among the isolates.

Evaluation of Genetic Diversity in Antiaris toxicaria Lesch. from Sacred Groves of the Western Ghats, India

Antiaris toxicaria Lesch. is a deciduous tree belongs to the family Moraceae, is native to the Old World tropics. It is an important industrial forest plant for its veneer, plywood and medicinal values. In the present study, genetic diversity of different populations of A. toxicaria collected from sacred groves of the Western Ghats, India has been evaluated. Thirteen RAPD and ten ISSR primers produced a total of 175 and 143 reproducible bands, respectively. RPI 10 of RAPD primers used showed maximum (0.49) polymorphic information content (PIC), while UBC 809 (0.37) exhibits maximum PIC among ISSR primers. Nei’s genetic similarity showed that pairwise similarity coefficients ranged from 0.460 to 0.832 in RAPD analysis, whereas 0.550–0.842 in ISSR analysis. Understanding the genetic diversity among natural A. toxicaria populations will be useful for effective long-term conservation.

Genetic Diversity Analysis in <i>Grevillea robusta</i> using ISSR Molecular Markers

The present study aimed to analyze genetic diversity using inter simple sequence repeat (ISSR) molecular markers among eleven genotypes of Grevillea robusta collected from Haridwar, Uttarakhand. Out of the total 108 bands generated with 11 ISSR primers, 104 were found to be polymorphic. The percentage of polymorphic bands at genetic level was 96.30%. The mean value of expected heterozygosity and unbiased heterozygosity were 0.290 and 0.305, respectively. Jaccard's similarity value ranged from 0.398 to 0.790. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering segregated the genotypes into two major clusters based on the pair-wise similarity coefficient. Clustering pattern revealed by UPGMA dendrogram was also supported by Principal Coordinate Analysis (PCoA). In the PCoA plot, 26.76% and 17.16% of total genetic variation were accounted by first and second coordinate, respectively. The higher level of genetic diversity was revealed by the values 0.445 ± 0.20 and 0.290 ± 0.16 recorded as Shannon's Information Index (I) and expected heterozygosity (H ), respectively. Therefore, the present E study reflects that a sufficient variability exist in the sampled germplasm and genetic improvement work could be very much effective in G. robusta for utilization in future agroforestry programme of the country.

EFFICACY OF MOLECULAR DIAGNOSIS TO DETERMINE GENETIC DIVERSITY AMONG INDIGENOUS ISOLATES OF Erwinia carotovora UNDER EGYPTIAN CONDITION

Thirty-Four isolates of Erwinia carotovora subspecies carotovora (Ecc) causing soft rot of potato, were collected from tubers of potato plants grown in North and East Egypt. The frequency of the isolated species of soft rot-associated bacteria, being 10, 10, 8 and 6 isolates from Governorates of Sinai, Sharqia, Gharbia and Beheira, respectively. The isolates were identified as Ecc by biochemical method and molecular identity then was confirmed by polymerase chain reaction (PCR) using specific primers FEc1 and REc1 which amplified the Eca-specific band of 690-733 bp. Pathogenicity test divided these 9 isolates into 3 aggressiveness groups, High infection (2 isolates), moderate infection (5 isolates) and low infection (2 isolates), receptively. These isolates were also characterized using the technique of Inter Simple Sequence Repeats polymerase chain reaction (ISSR-PCR) found that 61 amplified fragments, 56 were polymorphic (91.8%) and the percentage of polymorphism ranged from 100% (844B) to 84.62% (HB12); the fragment sizes were 224bp to 1.36 kb. The unweighted pair-group method with arithmetical average (UPGMA) cluster analysis based on pairwise genetic similarity coefficient revealed that the similarity between the selected 9 soft rot bacterial isolates ranged from 0.125 between Ec6 and Ec9 to 0.875 between Ec1, Ec3 and Ec4. The average of similarity among genotypes was 0.500 and divided the soft rot isolates into three well-defined clusters showing a great level of genetic diversity. However, these clusters were not specific to aggressiveness groups, origin or special potato variety. Isolates with different aggressiveness levels, originated from different potato varieties participate between the same clusters. This means that the isolates likely derived from the same source population and got scattered from one area to another through their hosts.

Development and diversity of lactic acid producing bacteria and bifidobacteria in healthy full term Indian infants from Himachal Pradesh.

Background/AimsThe initial microbial colonization is a crucial step for the healthy development of an infant. Previous studies from India reported the dominance of target microbial species among Indian infants without any analysis on the diversity of target groups. This is the first study from India with an objective to investigate the establishment and diversity of lactic acid producing bacteria (LAB) and bifidobacteria in vaginally delivered, full term, breastfed infants for the first 4 months after birth.MethodsPresent study used polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) based sequence analysis of LAB and bifidobacteria in healthy infants. The results were used to compare the development and early colonization by LAB and bifidobacteria using diversity indices during the initial months of development of gut microbiota in infants.ResultsDuring the first 4 months, the Shannon diversity index (H) of LAB increased from 1.16 to 1.318 and for bifidobacteria the H increased from 0.975 to 1.293 (P<0.05). Higher Sorenson’s pair wise similarity coefficient was observed for LAB and bifidobacteria during 2nd and the 3rd month. The species of the genera Enterococcus, Streptococcus, and Lactobacillus were dominant among the LAB group whereas Bifidobacterium breve was dominant species among Bifidobacterium group.ConclusionsOur results indicate that in breast fed infants, the microbial diversity of LAB and bifidobacteria increased during the period of study.

Genetic Diversity among Isolates of Phytophthora sojae in Anhui Province of China based on ISSR-PCR Markers

To explore genetic differentiation and the genetic relationships of Phytophthora sojae in Anhui Province, the inter-simple sequence repeat (ISSR) technique was used to analyze the genetic diversity of P. sojae. One hundred and sixty ISSR fragments were observed, including 129 (80.6%) polymorphic bands. This suggested that abundant genetic diversity existed among P. sojae in Anhui Province. The pairwise genetic similarity coefficients among the 62 strains ranged from 0.72 to 0.96, with a mean value of 0.85, indicating that there was a high level of genetic variation. Phytophthora sojae strains were divided into five clusters based on neighbor-joining (NJ) analysis, and the clustering was not related to geographic source, according to Mantel’s test (r = 0.3938). In addition, the clustering of strains from the same geographical source had little relationship to the year of collection. Analysis of molecular variance (AMOVA) showed that 16.65% of the genetic variation was derived from the collection area and 83.35% of the genetic variation was within-population variation. The genetic flow between different geographical sources ranged from 0.623 to 2.773, with a mean of 1.325, suggesting that gene exchange was frequent. Genetic distance and the genetic differentiation coefficient were not related to spatial distance.

Molecular marker analysis of genetic diversity in relation to reproductive behaviour of Commiphora wightii populations distributed in Gujarat and Rajasthan states of India

Guggul (Commiphora wightii) is a critically endangered medicinal plant distributed in arid and semi-arid agro-climatic zones of Northern-west India. Information on genetic diversity of C. wightii using DNA markers even though reported is limited to Rajasthan and Haryana populations and that too without considering its reproductive behaviour. In the present study, we are reporting for the first time the genetic diversity vis-a-vis its reproductive behaviour by including more number of accessions from Gujarat, which is the only place in India where sexual populations are distributed. We used RAPD and ISSR markers since genome sequence information is lacking in the species. Twenty four RAPD primers and 16 ISSR primers amplified a total of 185 and 128 reproducible DNA fragments, respectively with fragment sizes ranged from 200 to 3000 bp. RAPD analysis showed higher polymorphism (80%) in comparison to ISSR (69%). Jaccard's coefficient of similarity showed that pair-wise genetic similarity coefficients ranged from 46 to 98.3% in RAPD analysis, whereas it ranged from 47.8 to 98.6% in ISSR analysis. The results showed that the trend of genetic variation was not strictly correlated to the geographical locations, but was related to the reproductive behaviour of the populations. The diversity was somewhat low in Rajasthan populations where only apomictic populations are distributed. Populations of maximum genetic diversity along with sexual forms were found distributed in Gujarat populations, especially in Kutchh, Dwarka, Jamnagar and Porbandar populations. Hence the study indicated these areas as the original areas of the species distribution from where it was spread to the other parts of Gujarat and Rajasthan.

Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean

Abstract Both RAPD and protein markers were to estimate genetic diversity present in eight varieties of soybean. Of the nineteen random primers used fourteen produced 83 bands 62 being polymorphic generating polymorphism of 74.69% level. Similar level of (72.58%) polymorphism was generated by 12 pair-wise combinations of primers. Five of the paired combinations did not generate banding patterns. Two of the paired combination (OPC-5 + OPC-15) and (OPC-5 + OPC-17) produced unique banding patterns for all the eight varieties. The bands generated by paired combinations of primers were common to one of the primers in 21% cases however 79% of them were found novel and can be used to reveal additional polymorphism. The polymorphism generated by SDS-PAGE remained very less compared to RAPD analysis. The estimation of pairwise similarity coefficient using Jaccard's similarity index based on RAPD revealed approximately 70% similarity among the genotype studied that is diversity being 30% only. Average similarity shown by SDS-PAGE was much higher (81%) than RAPD based similarity estimates. The clustering based on UPGMA analysis of RAPD profiling separated all the varieties whereas SDS-PAGE grouped three varieties together at 100% similarity. Thus, it was concluded that the material though comes from diverse sources but had narrow genetic base.

Assessment of Genetic Variability in Pistachio (Pistacia vera L.) with Nuclear SSR Molecular Markers

Pistachio (Pistacia vera L.) is considered to be the most widely cultivated species in the genus Pistacia and regarded as the most probable ancestral species within the genus. As one of the oldest nut crops in human history, pistachio nuts have a high nutritional value and are commercially important. In the present study, the genetic variation of pistachio genotypes was investigated by nuclear SSR markers. The transferability of the SSR markers was high across genotypes, thus, flanking regions of the SSRs are conserved in the studied genotypes. High level of polymorphism was detected among the studied genotypes. The seven SSR primer pairs generated a total of 18 alleles that 13 of them were polymorphic among the genotypes. The range of the polymorphic alleles was 1 (for Ptms9, Ptms40, Ptms41, and Ptms42) to 5 (for Ptms7 locus) with an average of 2.57. The amplified allele sizes ranged from 120 to 250 bp. Pair-wise genetic similarity coefficients varied from 0.20 to 0.75. The UPGMA dendrogram differentiated the genotypes into two major clusters. The present results may be used for the conservation, core collection and future breeding of the pistachio.

Molecular Identification and Genetic Diversity Analysis of Chinese Sugarcane (Saccharum spp. Hybrids) Varieties using SSR Markers

Sugarcane (Saccharum spp. hybrids) is an important sugar and renewable bio-energy crop with a high aneu-polyploidy and complex genome. The complex characteristics of sugarcane genome enhance the difficulty of selecting elite varieties in sugarcane breeding program. The objectives of this study were to establish the molecular identities (ID) of 91 nationally or provincially released Chinese sugarcane varieties and to evaluate the extent of genetic diversity among these varieties using SSR DNA markers and two fingerprinting systems, i.e., capillary electrophoresis (CE) and polyacrylamide gel electrophoresis (PAGE). A total of 151 SSR alleles together with 20 new alleles were detected by CE and 117 SSR alleles were detected by PAGE. Primer pairs SMC336BS, SMC31CUQ, and SMC597CS amplified more than eight alleles detectable by either CE or PAGE. Polymorphism information content (PIC) values of the SSR markers varied from 0.71-0.98 with an average of 0.90 for CE, or from 0.55-0.95 with an average of 0.84 for PAGE. UPGMA method classified the 91 varieties based on the CE data into four major groups with pair-wise similarity coefficients ranging from 58% to 95%. The genetic similarity estimates within and between the four groups varied from 0.31 to 0.87, with a mean of 0.49. Our results illustrated that the 21 SSR primer pairs in combination with CE or PAGE detection system could be a very useful working tool for molecular identification of sugarcane varieties, genetic diversity assessment, and parental selection in sugarcane breeding.

Genome-wide assessment of genetic diversity and fiber quality traits characterization in Gossypium hirsutum races

Gossypium hirsutum races are believed to be potential reservoirs of desirable traits, which can play crucial roles to overcome the existing narrow genetic base of modern Upland cotton cultivars. However, prior to utilizing the races in cotton improvement programs, understanding their genetic constitutions is needed. Thus, this study used molecular and morphological techniques to characterize 110 G. hirsutum germplasm including 109 semi-wild accessions and one Upland cotton cultivar, CRI12. In the study, 104 SSR markers detected 795 alleles, with an average of 7.64 alleles per marker, ranging from 3 to 14, and average polymorphism information content (PIC) value of 0.71. And 96 of the markers were found to be highly informative, with PIC value≥0.50. Pairwise genetic similarity coefficient across the accessions ranged from 0.19 to 1.00, with an average value of 0.46. Morphological characterization was done using fiber length, fiber strength, micronaire, fiber uniformity index, and fiber elongation. Pairwise taxonomic distance within the accessions ranged from 0.17 to 3.41, with a mean of 1.33. The SSR and fiber quality traits data set based unweighted pair group method of arithmetic mean (UPGMA) analysis grouped the accessions into 7 and 12 distinct clusters, respectively, that corresponds well with the results of principal component analysis (PCA). Our study revealed the existence of vast molecular and morphological diversities within the accessions and provided valuable information on each semi-wild accession for quick and better informed germplasm utilization in cotton breeding programs.

Molecular assessment of genetic diversity among accessions of medicinal shrub Nyctanthes arbor-tristis (L.) from north and central India

Molecular characterization of 16 accessions of Nyctanthes arbor-tristis L. collected from different eco-geographical regions of north and central India was carried out to assess genetic diversity using RAPD markers. During RAPD analysis, amplification of genomic DNA of 16 accessions by 40 random primers generated 275 scorable bands with an average of 8.59 bands per primer, of which 180 (65.45%) bands were polymorphic and 95 (34.54%) bands were monomorphic. Each primer generated a unique set amplification product ranging in size from 200 to 2200 bp. The number of bands produced per primer ranged from 4 to 13. The PIC value ranged from 0.703 to 0.909 with an average of 0.848. The RAPD based Jaccard's pair-wise genetic similarity coefficient for Nyctanthes accessions ranged from 0.873 to 0.680. The association amongst different accessions was presented in the form of UPGMA generated dendrogram which clearly segregated all the 16 accessions into two major clusters with equal number of genotypes in each cluster. The major clusters ‘A’ and ‘B’ were further divided into two sub-clusters. The results obtained indicated that N. arbor-tristis accessions, collected from diverse, possessed moderate level of genetic diversity and this information can be further used for the improvement of Nyctanthes for various traits through different breeding methods.

Molecular Variability of &amp;lt;i&amp;gt;Fusarium verticillioides&amp;lt;/i&amp;gt; (Sacc.) in Maize from Three Agro-Ecological Zones of Southwest Nigeria

This study investigated the characterisation of Fusarium verticillioides strains using Amplified Fragments Length Polymorphism (AFLP) EcoR1-G/Mse1-C primer combination. This was done to determine the amount of genetic variability present in F. verticillioides population. The objective of this study is to carry out molecular characterization of F. verticillioides strains from infected ear of maize. Six isolates were obtained in maize ear from 10 locations in three agro-ecological zones of Southwest Nigeria. Polymorphic bands detected were 164 from one base extension of EcoR1 and Mse1 primers in the selective amplification. Primer combination EC + MC produced the highest polymorphic bands of 58, while primer combination ET + MC had the highest percentage polymorphism (100%). Genetic similarity (67%) was observed among strains from Ibadan (IBD) (34, 36), Igbooho (IGH) (39), Ado-Ekiti (EKT) (46, 47), Saki (SAK) (52) and Igboora (IGB) (57, 58, 59 and 60). Strains 19 and 20 from Ilesha (ILH) had the highest pairwise similarity coefficient at 97% grouped in cluster II. The dendrogram delineated F. verticillioides strains into four major cluster groups with 77% similarity and other sub-groups within. Fusarium verticillioides strains could therefore be heterogeneous, and thus amplified fragment length polymorphism is an ideal tool for distinguishing the pathogenic variants of Fusarium verticillioides.

Genetic structure and relationships of an associated population in ramie (Boehmeria nivea L. Gaud) evaluated by SSR markers

ABSTRACTRamie (Boehmeria nivea L. Gaud) is one of the most important natural fibre crops. For enhanced crop development, it is necessary to understand its population structure and genetic relationships. In this study, we assessed the genetic diversity and population structure of 134 ramie accessions (with three plants per accession) from 12 regions by using 36 simple sequence repeat markers. The 36 microsatellite primers revealed 149 alleles in 134 ramie populations, with an average of 4.14 alleles per locus. The structure analysis divided the 134 ramie accessions into three groups (I, II and III), and into further six subgroups (a, b, c, d, e and f). In Subgroup b, 13 accessions were from Guizhou Province, 9 accessions were from Sichuan Province and the remaining 20 accessions were from Chongqing (4), Hunan (8), Guangxi (4), Jiangxi (2), Yunan (1) and Taiwan (1). In Subgroup d, 22 accessions were from Guizhou Province and the remaining 17 accessions were from Chongqing (6), Sichuan (5) and Yunnan (6). It can be inferred that the genetic background of these ramie accessions did not always correlate with their geographical regions. Similar results were found in Subgroups a and f. The pair-wise genetic similarity coefficients between the 134 accessions ranged from 0.390 to 0.939, which suggested that there was abundant genetic diversity in the ramie accessions. These markers have provided important information about the genetic structure of ramie, which can contribute to future breeding and improvement programmes for these resources.