Polymorphism Information Content Research Articles

Genetic diversity studies between Ipomoea wild species and cultivated sweet potato (Ipomoea batatas (L.) Lam.) using SSR markers

Sweet potato (Ipomoea batatas (L.) Lam) is one of the major tuber crops in Asian countries, including India, yet the interrelationship and genetic variability among the cultivar and its crop wild relatives remain obscure. The wild relatives of sweet potato represent a vital source of untapped genetic diversity in the breeding programs. In this study, a set of 12 Simple Sequence Repeats (SSR) markers were utilized to understand the extent of genetic diversity and relationship within and between 20 sweet potato accessions, 23 wild Ipomoea species and two Merremia species for utilization in breeding programmes. The SSR primers produced 84 polymorphic alleles within the range of 105-393 bp, collectively showing an average polymorphism of 94.5%. The average Polymorphic Information Content (PIC) value of 0.67 showed that all the primers were polymorphic in nature. Similarity coefficient based dendrogram and Principal Component Analysis (PCA) scatter plot clearly differentiated all the cultivars and wild species. The cluster dendrogram analysis revealed the close relationship of cultivars with I. triloba and I. trifida at a similarity index of 0.75. Our analysis showed a high degree of genetic variability within and between hexaploid sweet potato and diploid wild species, whereas lower within the cultivars, which shows that there is a high level of genetic diversity exists within the Ipomoea species for its utilization in breeding programs. Thus, the two wild species, I. trifida and I. triloba could be used in hybridization for improvement of sweet potato through ploidy manipulation.

Molecular Identification of Genetic Diversity and Population Structure in Moroccan Male Date Palm (Phoenix dactylifera L.) Using Inter-Simple Sequence Repeat, Direct Amplification of Minisatellite DNA, and Simple Sequence Repeat Markers

Understanding genetic diversity and population structure plays a vital role in the efficient use of available material in plant-breeding programs and in germplasm conservation strategies. In the present study, we aim to evaluate the genetic variations and population structure of male date palms from Morocco. The genetic diversity of 100 date palm (Phoenix dactylifera L.) genotypes was investigated using the performance of three types of molecular markers: inter-simple sequence repeats (ISSRs), direct amplification of minisatellite DNA (DAMD), and simple sequence repeats (SSRs). On the basis of their polymorphic information content (PIC) (ISSRs = 0.38; DAMD = 0.4; SSRs = 0.33), effective multiplex ratio (EMR) (ISSRs = 27.34; DAMD = 52.31; SSRs = 22.20), Resolving power Rp (ISSR = 13.81; DAMD = 28.73; SSR = 14.6), and marker index (MI) (ISSRs = 9.22; DAMD = 20.23; SSRs = 7.54) values, all markers used in our study are considered informative markers. Among them, DAMD markers demonstrated slightly higher informativeness compared to ISSR and SSR markers. A total of 216, 438, and 248 bands were, respectively, detected using ISSRs, DAMD, and SSRs, with 95%, 98% and 94% of polymorphism, respectively. The AMOVA results revealed considerable diversity within date palms. The PCOa results showed that males of Tinghir and Errachidia were regrouped into the same cluster, while males of Goulmima were separated into another group. A cluster and structure analysis separated the studied genotypes into three groups. One group comprises genotypes of males from Zagora with some female varieties scattered in this group. The second group includes male genotypes from Goulmima along with accessions of female and male varieties. The third group contains males of Errachidia, Tata and Tinghir populations. The cluster and structure analysis separated the studied genotypes according to their origin.

Development and characterization of novel EST-SSR markers for Gentiana straminea Maxim., a traditional Tibetan herb in China and cross-amplification in related species

Abstract Gentiana straminea Maxim. (Gentianaceae) is an important traditional Tibetan herb that is mainly distributed on the Qinghai-Tibetan Plateau. Despite its agricultural and pharmacological importance, there remains a paucity of microsatellite markers, particularly expressed sequence tag-simple sequence repeat (EST-SSR) markers, available for this local endemic species. In this study, based on previous Illumina transcriptome data of G. straminea, a total of 96 EST-SSR markers were initially designed and tested. Thirty-two of 96 loci (33.33%) were successfully amplified and verified for validation. Among them, 10 were polymorphic and had clear bands. The polymorphism information content values were 0.09–0.799, the number of alleles per locus ranged from 3 to 14, and the levels of observed and expected heterozygosity were 0.078–0.722 and 0.238–0.884, respectively, which suggested a high level of information. Moreover, cross-amplification was successful for 10 loci in two other related species, Gentiana macrophylla Pallas and Gentiana dahurica Fischer. These EST-SSR markers provide a valuable tool for investigating the genetic diversity related to quantitative traits and population genetic studies on G. straminea and related species in sect. Cruciata Gaudin.

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology.

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

Construction of a DNA Fingerprint Map and a Core Collection of Platycladus orientalis

Platycladus orientalis is one of the main species used in afforestation projects in the arid mountains of north and northwest China, meaning that the species has high ecological and economic value. Studying its genetic diversity and obtaining a core germplasm base and genetic fingerprint data are important for the screening, development, and utilization of the species. This can provide the core materials for the preservation and evaluation and mining of germplasm resources and can provide superior gene resources for breeding programs. In this study, the genetic diversity among 104 P. orientalis germplasm resources was examined using simple sequence repeat (SSR) markers, and a core germplasm containing 31 accessions was constructed that represents the most genetic diversity of P. orientalis accessions. Each of 20 pairs of primers showed polymorphism, and 117 alleles were identified. The average number of alleles at each locus was six, and the mean effective allele number was 2.607. The average Shannon’s information index was 0.983, and the average polymorphism information content was 0.445. There is thus a significant amount of genetic variation within P. orientalis germplasm, yielding a rich genetic diversity. The constructed core germplasm accounted for 30% of the original germplasm. There was no significant difference in genetic diversity between the core germplasm and the original germplasm resources, indicating that the obtained core germplasm resources could fully represent the original germplasm. Using 17 SSR primers with high polymorphism, the DNA fingerprints of 104 P. orientalis germplasm resources were constructed. The results showed that 98 had specific DNA fingerprints. The results of this study provide a valuable basis for the collection, preservation, and utilization of P. orientalis germplasm resources, and the methods adopted in this study have important reference value for the construction of core germplasm of other perennial woody plants.

A Comprehensive Molecular, Biochemical, Histochemical, and Spectroscopic Characterization of Early and Medium Duration Rice Genotypes Investigating Dry Matter Accumulation Efficiencies.

Investigation on accumulation of cell wall components over critical growth stages will surely provide a new insight into dry matter accumulation studies in rice. An elevated biomass production provides an alternative strategy of yield improvement, which in turn maneuvers the species concerned as potential dual-purpose crop. On that note, present study was carried on 33 early and 39 medium duration rice genotypes. The average cellulose accumulation was 6.51% and 8.17% in early and medium duration genotypes, respectively, at flowering stage, which later on dipped to 1.43% and 3.46%, respectively, at physiological maturity. The gene specific marker MDgsp-5.a exhibited highest estimate of polymorphic information content (PIC), i.e., 0.685, closely followed by MDgsp-6.a with polymorphic information content (PIC) of 0.683. The control genotypes, i.e., Pratap and Mandakini, are grouped under the same cluster, i.e., Cluster-I.A, indicating their inherent genetic divergence from that of potential accumulators pertaining to cellulose accumulation. Pratap and Mandakini failed to produce peaks of conspicuous form at 3342cm-1 and 1635cm-1, bearing out by their low performance pertaining to cellulose and lignin accumulation at the later stages of development, respectively. From histochemistry studies, it was observed that the cell walls of sclerenchyma, peripheral vascular bundles, and parenchyma of the culm transections in control genotypes stained lightly than that of prolific accumulator cell walls, thus corroborating the findings of compositional analysis. The variation in cell wall thickening is primarily accounted due to altered carbohydrate accumulation across the growth stages as explored under scanning electron micrograph.

Genetic Characterization of Water Yam (Dioscorea alata L.) and Production Constraints of Yam in Pwani Region and Unguja Island, Tanzania

Yam (Dioscorea spp.) is a tuber crop cultivated in over 30% of all regions in Tanzania, contributing to the carbohydrate needs of many households. The morphological and genetic diversity of water yam (D. alata L.) local cultivars collected from Pwani region and Unguja Island were evaluated using 26 agro-morphological characters and 10 Short Sequence Repeat (SSR) markers. Cluster analysis using morphological characters classified nine water yam local cultivars into two main clusters with three subclusters. Tuber flesh and leaf colour were the main descriptors for clustering. The genetic diversity of 128 water yam genotypes using ten polymorphic SSR markers generated a total of 40 alleles that ranged from 2 to 7 per SSR marker. The mean polymorphic information content (PIC) ranged from 0.3 to 0.9, with a mean of 0.56. Cluster analysis separated 128 yam genotypes into two main clusters with five subclusters. The findings revealed relatively high genetic diversity of D. alata in the study areas. A structured questionnaire revealed drought (29.3%) and lack of planting materials (23.3%) as the major constraints to yam production in the study areas. Information reported in this study is useful in improving, reviving and promoting yam through breeding and conservation programs.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Molecular characterization of some currants (Ribes species) from Türkiye using inter-primer binding site (iPBS) and simple sequence repeat (SSR) markers

AbstractThis study was carried out to determine the genetic relationships and variation levels among currant genotypes and cultivars in Türkiye. Ten currant cultivars and one hybrid Jostaberry cultivar, which are breeding products of Europe but are best known and have high commercial value in Türkiye, were used. One black-fruited currant cultivar from Türkiye was included. In addition, 14 currant genotypes naturally grown in Türkiye were used. In this study, 14 retrotransposon-based inter-primer binding site (iPBS) and 10 microsatellite-based simple sequence repeat (SSR) markers were used for a total of 26 currant samples. By evaluating the allele profiles obtained from PCR and capillary electrophoresis with iPBS and SSR primers, the size range, average number of alleles, total number of alleles, number of polymorphic alleles, polymorphism rate, heterozygosity, polymorphism information content, marker index and discriminating power were determined successfully. In addition, unweighted pair group method with arithmetic mean (UPGMA) dendrograms and principal coordinate analysis (PCoA) were constructed and performed. The amounts of amplification product produced using iPBS and SSR markers for currant species with different fruit colours were also compared. In this study, it was proven that the level of genetic relatedness among currant cultivars and genotypes can be determined with high accuracy by iPBS markers. Moreover, the use of iPBS markers in currants was performed for the first time in this study. On the other hand, with the preferred SSR markers, the level of genetic relatedness among currants was successfully determined.

Genetic diversity assessment of Trichoderma spp. isolated from various Egyptian locations using its gene sequencing marker, rep-PCR, and their cellulolytic activity

BackgroundThe phylogenetic relationships and phylogeny of twenty-six Trichoderma species collected from various Egyptian locations were investigated. The genetic diversity among the examined isolates was tested using the rep-PCR marker. Trichoderma species were screened for their cellulase activities.ResultsThree isolates demonstrated highly significant FPase activities, namely MNF-MAS-Tricho 1, MNF-MAS-Tricho 2, and MNF-MAS-Tricho 3 (0.50, 0.39, and 0.49 IU ml−1, respectively). MNF-MAS-Tricho1 showed the highest significant CMCase activity (0.80 IU ml−1). Concerning β-glucosidase, MNF-MAS-Tricho 1 was the highest (0.78 IU ml−1), while MNF-MSH-Trich 11 and MNF-MAS-Tricho 15 were the lowest (0.36 IU mL−1). The percentage of polymorphism ranged from 46.15 to 83.33%. (GTG)5 marker produced the greatest number of polymorphic loci (13 loci out of 18 loci) with about 83.33% polymorphism, followed by rep-10 with 69.2% polymorphism. Furthermore, the polymorphism information content (PIC) estimates ranged between 0.285 for Rep-10 and 0.340 for (GTG) 5 with an average of 0.306. The tested primers exhibited high discriminating and resolving powers.ConclusionThe findings of this investigation were used to classify Trichoderma species, evaluate their genetic variability using ITS sequencing, rep-PCR, and measure their cellulase activities. These markers can facilitate more rapid and less complicated studies of Trichoderma population dynamics and evaluate their establishment after release into agricultural environments. The results will help to evaluate the genetic diversity of Trichoderma in future research.

Genetic background of lily germplasm resources based on SSR markers

To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.

Decoding genetic diversity and population structure of Brassica species by inter primer binding site (iPBS) retrotransposon markers

AbstractMarker-assisted breeding serves as a potent tool for screening target germplasm, assessing genetic diversity, and determining breeding potential of a crop. Therefore, inter primer binding site (iPBS)-retrotransposons marker system was employed to evaluate a collection of 33 Brassica genotypes, including 10 Brassica juncea, 5 B. oleracea, 7 Sinapis alba, 5 B. nigra, and 6 B. rapa, were utilized to evaluate their genetic diversity and variations 10 polymorphic primers that generated a total of 144 bands. Various diversity indices were calculated in the studied germplasm, including polymorphism information content (0.13–0.30), effective number of alleles (1.217–1.689), Shannon’s information index (0.244–0.531), and gene diversity (0.148–0.370). These indices collectively affirmed substantial genetic variations within the germplasm. Molecular variance analysis revealed that the majority (62%) of genetic variations were present within populations. The Brassica accessions were categorized into three populations utilizing a model-based structure algorithm. Evaluation of diversity indices based on the structure indicated that populations III and II exhibited higher diversity. Principal coordinate analysis and neighbor-joining analysis further corroborated the three distinct populations, confirming the reliability of the STRUCTURE analysis. Notably, the genetic distance assessment identified BN1 and BN3 from B. nigra species and the genotypes BO1 and BO3 from B. oleracea as genetically diverse mustard accessions. The extensive genetic diversity observed within the Brassica germplasm underscores its significance as a valuable genetic resource for comprehensive Brassica breeding programs. Moreover, these accessions hold promise as suitable candidates for heterosis breeding initiatives aimed at improving mustard production.

Identification and characterization of functionally relevant SSR markers in natural Dalbergia odorifera populations

BackgroundDalbergia odorifera is a rare and precious rosewood specie, which is valued for its amber tones, abstract figural patterns, and impermeability to water and insects. However, the information on genetic diversity and marker-assisted selection breeding of D. odorifera is still limited. Simple sequence repeat (SSR) markers are an ideal tool for genetic diversity analysis and marker-assisted molecular breeding for complex traits.ResultsHere, we have developed SSR markers within candidate genes and used them to explore the genetic diversity among D. odorifera germplasm resources. A total of 635 SSR loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 52.28%, 22.99% and 21.42%, respectively. From these, a total of 114 SSR primers were synthesized, of which 24 SSR markers displayed polymorphism (polymorphic information content (PIC) > 0.25). Subsequently, these polymorphic markers were used for the genetic diversity analysis of 106 D. odorifera individuals from 11 natural populations. According to the genetic diversity analysis of D. odorifera natural populations, the average observed heterozygosity (Ho) was 0.500, the average expected heterozygosity (He) was 0.524, and the average Shannon’s information index (I) was 0.946. These indicated that the natural populations had moderate genetic diversity. AMOVA analysis showed that 5% of the total variation was within the individuals of a population, whereas 95% of the variation was among the individuals of the populations, indicating a high degree of genetic variation between populations. On the basis of their genetic structures, these populations could be divided into four groups.ConclusionsOur study provides important experimental resources for genetic studies and assists in the program of molecular breeding of D. odorifera wood formation.

Genetic structure and molecular analysis of the species of the genus Artemisia L. (Asteraceae) distributed in Azerbaijan

In this study, the phylogenetic relationships and genetic structure of 10 collected genotypes of Artemisia szowitziana (Besser) Grossh and Artemisia fragrans Willd. species from different regions of Azerbaijan were investigated using RAPD primers. A total of 94 amplicons were amplified using selected RAPD primers. Among them 3 band with OPA-02 primers and 12 band with OPW-17 primers were amplified. The highest polymorphism among the investigated RAPD markers was 100, 90.91 and 90%, which has been obtained by OPW-17, OPT-19, and OPT-20 primers, respectively. However, the calculated average value of polymorphism was as high as 72.79% based on 10 different RAPD markers. The average PIC (Polymorphism Information Content) value (0.864) has indicated the rich genetic diversity among the studied samples. The cluster analyses by using Jaccard similarity index and UPGMA method classified all Artemisia L. samples into 6 major groups. Principal Component Analysis (PCA) justified 74.22% of the total variance. Based on the results obtained, it has been observed that there is a wide range of diversity in the molecular level between the population of Artemisia szowitziana (1-2 and 4-6 samples) and Artemisia fragrans (3, 5, 7 and 8, 9, 10 samples) and between population of the Artemisia species in Azerbaijan.

Analysis of Elimination Effects of Inbreeding on Genotype Frequency in Larval Stages of Chinese Shrimp.

Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.

Development and utilization of genome-wide InDel markers in Sorghum [Sorghum bicolor (L.) Moench

Sorghum (Sorghum bicolor L. Moench) has become an increasingly valuable crop for food, feed, and especially bioenergy feedstock production, which makes the crop extremely attractive for studying genomics and genetic diversity. Molecular markers and genomics play essential roles in sorghum breeding. The rapid development of next-generation sequencing technology has facilitated the identification of genome-wide insertion-deletion (InDel) polymorphisms, enabling the efficient construction of InDel markers that are suitable for user-friendly PCR. This study was conducted with the objective of discovering and developing InDel markers using double digest restriction site-associated DNA sequencing (ddRAD-Seq) data. A total of 19,226 InDels distributed across 10 chromosomes in the sorghum genome was identified. Of those, deletions constituted 65.7% while the remain was insertions. A comprehensive analysis of all the chromosomes revealed a total of 80 InDel sites with a minimum length of 10 bp. For a good conversion of the InDel regions to beneficial molecular markers, specific primers were designed for the amplification of 47 InDel regions that were selected for further investigation. A diverse panel of sorghum consisting of 16 accessions served a source for the developed InDel markers validation. Of the 47 InDel markers, 14 were tested across 16 sorghum accessions and were demonstrated their helpfulness for marker-assisted selection in sorghum. The polymorphic information content (PIC) values of the 16 markers varied between 0.11 and 0.38, with an average of 0.28. The findings of this study indicated that the identification of InDels and the development of molecular markers for sorghum were accomplished using the ddRAD-Seq data.

Development of polymorphic simple sequences repeats markers from whole gene resequencing data comparison of 68 Oncorhynchus mykiss

Rainbow trout (Oncorhynchus mykiss) is a significant cold-water fish farmed in China. Currently, most molecular marker-assisted breeding applications in rainbow trout rely on SSR markers. Although many rainbow trout SSR markers have been developed, methods for mining many polymorphic SSR markers from the genome and identifying them efficiently and rapidly are still lacking. For this reason, this study used in silico simulation method to rapidly develop a large number of polymorphic SSR markers quickly. A total of 354,613 SSR loci with two to six nucleotide repeat motifs were mined from 32 chromosomes of the rainbow trout reference genome using GMATA. The chromosome sequences of the reference genome were then aligned to the whole genome sequencing data (10×) of 68 rainbow trout samples. In silico genotyping was performed using the HipSTR programme to compare and count the variation in the number of repeats of the motifs of the SSR loci in the samples. The loci with high deletion rates and monomorphism were discarded, while those with more than one non-reference allele were kept. The final set of polymorphic SSR loci screened was 78,828. Finally, 4,821 SSR loci were selected with more than 3 alleles and no deletion in all rainbow trout samples and were physically mapped. The average polymorphic information content of these loci was 0.692, indicating high levels of polymorphism. These SSRs were utilized to analyse the genetic diversity and population structure of the 68 rainbow trout samples. The results showed that these 68 samples were divided into two groups. These newly discovered polymorphic SSR markers will provide valuable information for evaluating the construction of rainbow trout family lines for genetic diversity and improvement.

Genetic variation and structure of endemic and endangered wild celery (Kelussia odoratissima Mozaff.) quantified using novel microsatellite markers developed by next-generation sequencing.

Kelussia odoratissima Mozaff. (Apiaceae) is a native plant that has been traditionally consumed in Iran's food and pharmaceutical industries. Overharvesting of the taxon, especially at the beginning of the growing season, due to its considerable medicinal and economic value, is believed to be the main reason for the extirpating of this plant. The consequences of the severe anthropogenic impacts on the genetic diversity of populations are poorly known. In order to investigate the level of genetic variation and patterns of the genetic structure of K. odoratissima, we developed novel microsatellite markers using the 454 Roche next-generation sequencing (NGS) platform for the first time. Out of 1,165 microsatellite markers bioinformatically confirmed, twenty-five were tested, of which 23 were used to screen genetic variation across 12 natural populations. Our results showed that the average number of alleles per locus and the polymorphic information content (PIC) were 10.87 (range 7 to 27), and 0.81 (range 0.67 to 0.94), respectively. The mean observed and expected heterozygosities (± SD) across all populations were 0.80 ± 0.31 and 0.72 ± 0.14, respectively. The average pairwise FST among the populations was 0.37 (range 0.04 to 0.81). Bayesian and distance-based clustering, and principal coordinate analyses revealed at least four major genetic clusters. Although high level of structure can be explained by landscape topography and geographic distance, presence of admixed populations can be associated to seed or pollen dispersal. Contrary to expectations, the high level of genetic variation and lack of inbreeding suggest that overexploitation has not yet significantly purged the allelic variability within the natural populations in protected areas.

Ecology, genetic diversity, and population structure among commercial varieties and local landraces of Capsicum spp. grown in northeastern states of India.

Northeastern states of India are known for unique landraces of Capsicum spp. with geographical indications. However, little information is available about these valuable landraces of chillies. Surveys and collections were carried out in niche areas to find out their ecology and diversity through morphological traits and molecular analysis using microsatellite markers. Our result characterized the ecology of niche areas as cool (11.0°C-20.7°C) and humid (>60% relative humidity) climates for dalle-chilli (Capsicum annuum L.); mild-warm (12.2°C-28.6°C) and humid for king-chilli (C. chinense Jacq.); and cool to warm (11.3°C-33.1°C) and humid for bird's eye chilli (C. frutescens L.) during the crop period. The canonical correspondence analysis has shown the significant impact of temperature on the agro-morphological traits and distribution of the landraces in their niche areas. A wide variability was observed for different quantitative traits and yield attributing characters (fruit length, diameter, weight, and yield), showing high heritability (97.0%-99.0%), and genetic advance as a percentage of the mean (119.8%-434.0%). A total of 47 SSR markers used for the molecular analysis generated 230 alleles, ranging from 2 (HPMSE-7) to 10 (HPMSE-5), with an average of 4.89 alleles per locus. The average polymorphism information content was also high (0.61) and ranged from 0.20 (HPMSE-7) to 0.85 (CAMS-91). The observed average heterozygosity was lower than the expected value. Analysis of molecular variance has shown significant variation within (69%) and between (31%) of the populations of Capsicum spp. Based on Nei's genetic distance, bird's eye chilli and king-chilli were found to be closer to each other, whereas dalle-chilli, a tretraploid species, was closer to hot pepper (C. annuum). However, the flower size of dalle-chilli was large and found closer to king-chilli in color and differs from C. chinense due to the presence of calyx teeth. For quality traits, landraces king-chilli, dalle-chilli, and bird's eye chilli have shown 2.8, 2.0, and 1.4 times higher average capsaicin and 0.46, 0.25, and 0.22 times higher average oleoresin content over the hot pepper, respectively. The knowledge of ecology and diversity can be used in identifying new areas for production, selection of elite lines, conservation, and crop improvement.

Genetic diversity and morpho-physiological assessment of drought tolerance in rapeseed (Brassica napus L.) cultivars

AbstractWater deficit is one of the most important abiotic stresses constraining crop production in rapeseed. Understanding the mechanisms of adaptation to this stress is essential for the development and production of drought-tolerant genotypes. For this reason, this research study aims to investigate the importance of genetic diversity in identifying genotypes with a high degree of drought tolerance through assessing effectiveness of inter simple sequence repeat (ISSR) markers on 14 genotypes of rapeseed in a factorial design. Morphological and physiological characteristics were studied after the early stages of growth; in order to evaluate the genetic diversity among genotypes, 18 different ISSR markers were used. A total of 106 clear and scalable loci were amplified, of which 60 bands (56.6%) were polymorphic. The highest polymorphism information content belonged to marker number 9 with the amount of 0.365 (85.7%). Gene variation ranged from 0.081 to 0.365 and the rapeseed genotypes were divided into three groups by cluster analysis (unweighted pair group method with arithmetic mean method). The analysis of molecular variance showed that 70% of the total variation was observed within populations and 30% of this variation occurred among populations. In addition, t-test was used for comparing oil content percentage among different genotypes in control and stress levels. Adriana had the highest amount of seed oil with 36.47%, whereas Karaj 2 had the lowest amount with 27.28 and Cooper had the highest decrease in oil content percentage under stress conditions. Overall, the genotypes Likord, Hyola 401 and Sarigol 32 were identified as the most drought-tolerant.