Evaluation Of Genetic Diversity Research Articles

Evaluation of DNA markers for molecular identification of three Piper species from Brazilian Atlantic Rainforest.

Piper is one of two large genera in the Piperaceae, and with ca. 2600 species, is one of the largest plant genera in the world. Species delimitation and evaluation of genetic diversity among populations are important requisites for conservation and adequate exploitation of economically important species. DNA barcoding has been used as a powerful tool and a practical method for species characterization and delimitation. The present work aims to evaluate molecular markers for barcoding three Piper species native to Brazil: P. gaudichaudianum (“jaborandi” or “pariparoba”), P. malacophyllum (“pariparoba-murta”) and P. regnellii (“caapeba” or “pariparoba”). A reference DNA barcode library was developed using sequences of three candidate regions: ITS2, trnH-psbA and rbcL. Transferability of the microsatellite (SSR) primers Psol 3, Psol 6 and Psol 10, designed originally for Piper solmsianum, to the three Piper species was also evaluated. The discriminatory power of the markers was based on the determination of inter- and intraspecific distances, phylogenetic reconstruction, and clustering analysis, as well as BLASTn comparison. Sequences of ITS2 enabled efficient species identification by means of the BLASTn procedure. Based on these sequences, intraspecific divergence was lower than interspecific variation. Maximum Parsimony analyses based on ITS2 sequences provided three resolved clades, each corresponding to one of the three analysed species. Sequences of trnH-psbA and rbcL had lower discriminatory value. Analyses combining sequences of these regions were less effective toward the attainment of resolved and strongly supported clades of all species. In summary, robustly supported clades of P. regnellii were obtained in most of the analyses, based either on isolated or combined sequences. The SSRs primers Psol 3, Psol 6 and Psol 10 were shown to be transferable to P. gaudichaudianum and P. regnellii, but not to P. malacophyllum. Preliminary cluster analyses based on the polymorphism of the amplified products suggested that Psol 3 has lower potential than Psol 6 and Psol 10 for discrimination of Piper species.

Contrasting phylogeographic patterns of earthworms (Crassiclitellata, Lumbricidae) on near-shore mediterranean islands

Comparative phylogeography is a powerful methodological approach to understand the particular evolutionary phenomena that occur in islands. This method has been rarely applied to insular earthworm communities. These soil animals show a striking dichotomy in their phylogeographic patterns: deeply divergent, regionally structured linages and widely distributed, genetically homogeneous lineages. An intensive earthworm sampling campaign in the Southern France archipelago of Hyères served as an opportunity to check for the existence of these patterns in the framework of a near-shore, continental archipelago. Molecular barcoding (COI sequencing) was performed for earthworm communities of 31 localities, and the seven with more informative distributions were chosen for phylogenetic inference and genetic diversity evaluation. A time-calibrated phylogeny was obtained to estimate a temporal framework for colonization and divergence within the islands, and haplotype networks were used to visualize relationships between populations in detail. Four species (Allolobophora chlorotica, Aporrectodea nocturna, Scherotheca cf. dugesi and Scherotheca rhodana) showed clades restricted to the archipelago and hints of Plio-Pleistocene in situ divergence. The other three species (Aporrectodea rosea, Aporrectodea trapezoides and Eiseniella tetraedra) lacked geographic structure, being nested in clades with individuals from distant countries; their arrival to the archipelago appeared consistent with human-mediated introduction. These contrasting phylogeographic patterns are discussed in the context of paleogeographic events affecting the Mediterranean in the Late Tertiary-Quaternary and biological traits of earthworms, with biparental sexual vs parthenogenetic reproduction as the main factor explaining them.

Evaluation of Genetic Diversity of َAgronomic and Physiological Traits in Wheat under Two Field Environments

Evaluation of Genetic Diversity of َAgronomic and Physiological Traits in Wheat under Two Field Environments

Machine Learning for Plant Breeding and Biotechnology

Classical univariate and multivariate statistics are the most common methods used for data analysis in plant breeding and biotechnology studies. Evaluation of genetic diversity, classification of plant genotypes, analysis of yield components, yield stability analysis, assessment of biotic and abiotic stresses, prediction of parental combinations in hybrid breeding programs, and analysis of in vitro-based biotechnological experiments are mainly performed by classical statistical methods. Despite successful applications, these classical statistical methods have low efficiency in analyzing data obtained from plant studies, as the genotype, environment, and their interaction (G × E) result in nondeterministic and nonlinear nature of plant characteristics. Large-scale data flow, including phenomics, metabolomics, genomics, and big data, must be analyzed for efficient interpretation of results affected by G × E. Nonlinear nonparametric machine learning techniques are more efficient than classical statistical models in handling large amounts of complex and nondeterministic information with “multiple-independent variables versus multiple-dependent variables” nature. Neural networks, partial least square regression, random forest, and support vector machines are some of the most fascinating machine learning models that have been widely applied to analyze nonlinear and complex data in both classical plant breeding and in vitro-based biotechnological studies. High interpretive power of machine learning algorithms has made them popular in the analysis of plant complex multifactorial characteristics. The classification of different plant genotypes with morphological and molecular markers, modeling and predicting important quantitative characteristics of plants, the interpretation of complex and nonlinear relationships of plant characteristics, and predicting and optimizing of in vitro breeding methods are the examples of applications of machine learning in conventional plant breeding and in vitro-based biotechnological studies. Precision agriculture is possible through accurate measurement of plant characteristics using imaging techniques and then efficient analysis of reliable extracted data using machine learning algorithms. Perfect interpretation of high-throughput phenotyping data is applicable through coupled machine learning-image processing. Some applied and potentially applicable capabilities of machine learning techniques in conventional and in vitro-based plant breeding studies have been discussed in this overview. Discussions are of great value for future studies and could inspire researchers to apply machine learning in new layers of plant breeding.

Determination of Flower, Pod and Seed Characteristics Related to Yield Components in Forage Pea Genotypes

In this study which was carried out during the 2015 summer season in Eskişehir, the flower, pod and seed characters attributed to yield components were investigated in 12 forage pea genotypes. They showed significant differences in terms of agronomic and morphological (flower, pod, and seed) traits. The highest fresh hay yield with 2171 kg/da and plant height with 106.6 cm were obtained from Populasyon-1. Crackerjack had lower values in some flower traits such as, whereas the higher values of pod and seed traits were obtained from cv. Rose. In addition, Population-1 included in the higher value group for standard petal width, keel petal length, calyx tube and teeth lengths, and flower length. Although cluster analysis did not reflect agronomic traits, the clustering resulted in four groups. The first group consisted of Özkaynak 1, 2, and 3 and Taşkent, Töre, and Population-2, which were the standard petal colour violet, light, and dark violet. Population-1 had both violet and white standard petal; however, it was included in the second group together with white-flowered Ulubatlı and Ürünlü according to cluster analysis. While Rose and Gölyazı were in the third group, Crackerjack was in the fourth group alone. There was a highly significant positive correlation between fresh hay yield and both standard petal width and length and flower length. Consequently, a hopeful result for summer growing in Eskişehir condition was obtained from Population-1. It was suggested that some flower characters can be used for pre-selection of yield-related traits in the evaluation of genetic diversity of pea germplasm through morphological trait.

Genetic structure of different equine breeds by microsatellite DNA loci

Aim. Our work was aimed at the evaluation of genetic diversity of three domestic equine breeds which differ by the history of their formation and use. Methods. Genotyping of DNA samples of three breeds of horses, namely, Hucul (78 animals), Thoroughbred (51 animals) and Ukrainian Saddle Horse (152 animals), was conducted by 11 microsatellite loci, recommended by the International Stud Book Committee (ISBC) and the International Society for Animal Genetics (ISAG). The mathematical analysis involved parametric and non-parametric methods of statistics. Results. The results of polymorphism analysis of the gene funds for Hucul, Thoroughbred and Ukrainian Saddle horses by 11 microsatellite DNA loci were fi rst presented in Ukraine. It was demonstrated that the study of microsatellite DNA loci allows both determining the reliability of origin of pedigree animals and controlling population processes in different breeds and the polymorphy of the very breeds. Conclusions. The molecular and genetic analysis of equine breeds, differing by their provenance, demonstrated specifi cities of genetic structure of each breed, which correspond to the formation history of their gene funds. The populational-genetic analysis using different mathematical methods is recommended for the purposes of evaluating and forecasting microevolution processes, controlling gene fund formation both during the breeding work and within the system of preserving genetic biodiversity

Evaluation of genetic diversity in Lepidium sativum L. germplasm based on multivariate analysis

Lepidium sativum L. is a fast-growing and underutilized medicinal plant. The Indian system of medicinal and health recognized this plant as a source of several medicinal and nutraceutical molecules. The 94 accessions collected from different eco-geographical region of India were evaluated for two consecutive years to assess the level of genetic variability. The ANOVA revealed considerable variability for all the quantitative traits. The hierarchical clustering grouped all the accessions into 6 clusters. The clustering showed that majority of accessions i.e. 68 (72%) were genetically close as they grouped into three clusters (I, IV, V). The intra-cluster values ranged from 138.89 (cluster I) to 26.92 (cluster IV). The minimum inter-cluster distance was recorded 51.63 (between cluster III and IV), while the maximum inter-cluster distance was 361.02 (between cluster II and VI). The correlation among the traits were found to be of similar magnitude and direction for almost all the traits. The highest and lowest broad sense heritability was recorded for plant height (88.88%) and number of lateral branches (26.98%) respectively in first year, while in second year, the number of silique/plant (97.30%) and date of emergence (4.36%) respectively. The high estimates of genetic advance were noticed for all the traits except plant height, days of maturity and number of silique/plant. Through the present investigation diverse accessions have been identified that could utilized for further genetic improvement of Lepidium sativum.

Genetic diversity in leafy mustard (Brassica juncea var. rugosa) as revealed by agro-morphological traits and SSR markers.

Leafy mustard (B. juncea var. rugosa) constitutes an important group of vegetable mustard crops in India and is mainly cultivated in home-backyard and hilly regions of Uttarakhand and some North-eastern states. In the present study, various agro-morphological traits, physiological and biochemical traits along with SSR markers were used for genetic diversity evaluation in a germplasm collection of leafy mustard. This study revealed a significant variation among 59 accessions of leafy mustard in both qualitative and quantitative agro-morphological traits indicating the accessions' promising potential for consumption purpose and for use in breeding programs. Maximum variability was recorded for leaf area elongation rate (CV = 53.12%), followed by total plant weight (TPW) (CV = 50.63%) and seed yield per plant (CV = 44.33%). In molecular analysis, 155 SSRs evaluated resulted in 482 alleles and the number of alleles varied form 1 to 8 with an average of 3.11 alleles per marker. A total of 122 (78.70%) SSRs resulted into polymorphic amplicons. PIC value varied from 0.32 to 0.77 with an average value of 0.44 per SSR locus. The unweighted neighbour-joining-based dendrogram analysis divided all the 59 accessions into two major groups on the basis of both agro-morphological traits and SSR markers, whereas, three subpopulations/subgroups were predicted by population STRUCTURE analysis. AMOVA indicated the presence of more variability within population than among population. Overall, agro-morphologically better performing and genetically diverse genotypes have been identified which could be further used as donors for leafy mustard improvement programs.

Statistical analysis of genetic diversity using faba bean landraces database

Abstract. Evaluation of genetic diversity among landraces could be an invaluable aid related to the sustainable use of ex situ collections. Statistical methods are currently available for analysis of databases from investigation of stored germplasm. Faba bean (Vicia faba L.) is a self-pollinating with high percentage of foreign pollination legume crop with a great importance for food and forage due to its high protein content as well as the important role in soil fertility and nitrogen fixation. The local populations are well adapted to specific agro-climatic conditions in the growing areas and are a rich initial material for the breeding programs. The purpose of this study is to establish the genetic diversity of 21 Bulgarian faba bean landraces by important traits in order to review the current potential of conserved germplasm for its sustainable use. All genotypes, included in the study, are collected from expeditions in the country, recorded in the National Register for Plant Genetic Resources and long term stored at the National Genebank. They are characterized according to the International Faba Bean Descriptors. The cluster analysis results show a high genetic diversity in the collection and the variability of each studied trait is presented. The factor analysis, which complements the cluster analysis, gives a reason to group the genotypes with their features into groups that have a breeding value. Genetic diversity in the studied collection has been identified and some of the landraces could be included in future breeding programs.

Evaluation of genetic diversity of honey bee in Ukraine analyzed by the SSR-markers

Aim. The aim of the work was to analyze current genetic structure of honey bee populations in Ukraine that belong to different subspecies: A. meliffera meliffera, A. meliffera carnica, A. meliffera macedonica using microsatellite markers. Methods. SSR-analysis was used for evaluation of the honey bee polymorphism. Amplified fragments were fractionated by electrophoresis in non-denaturing polyacrylamide gel. DNA bands were detected using silver nitrate staining. Results. The analysis of the sample of honey bees (workers and male-bees) collected from different regions of Ukraine was performed by using two SSR-markers (Ac011 and A007). In this sample reasonably high polymorphism was observed, especially for the SSR-marker A007. Conclusions. It was estimated that SSR-analysis method can be applied in molecular-genetic analysis of honey bees for evaluation of genetic diversity and cross-subspecies hybridization.
 Keywords: microsatellite markers, Apis meliffera, PIC (Polymorphism Information Content).

Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Nephelium lappaceum L.) germplasm

The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.

Applications of molecular markers in Genetic Diversity Studies of maize

Molecular markers are efficient for exploiting variations in genotypes as they are not influenced by environmental factors and also speed up breeding programs. They are used to detect large numbers of distinct divergence between genotypes at the DNA level. Genetic diversity study helps to estimate the relationship between inbred lines to make the best hybrid combinations. Lines which are clustered in different heterotic groups are considered as the best hybrid combinations to carry out further breeding activities. Molecular markers are used to meet a number of objectives, including genetic diversity analysis and prediction of hybrid performances in divergent crop species. Agro-morphological and molecular markers have been utilized to study genetic diversity so far. In maize, the uses of molecular markers are important for the evaluation of genetic diversity of inbred lines and in clustering them into heterotic groups. These markers determine genetic similarity of the lines and are used to assess the genetic diversity of maize. Molecular markers have proven valuable for genetic diversity analysis of many crop species and genetically diverse lines are important to improve hybrid breeding.
 Keyword: Molecular marker; Genetic diversity; Genetic variation, Diversity Array technology; cluster analysis

The study of genetic diversity in a minicore collection of durum wheat genotypes using agro-morphological traits and molecular markers

The evaluation of genetic diversity in a gene pool contributes to the effective selection of genotypes and truncates the breeding time. In the present study, 96 durum wheat genotypes were evaluated for (1) genotypic diversity using two DNA marker systems: CAAT box-derived polymorphism (CBDP) and inter-simple sequence repeats (ISSR) markers and (2) phenotypic diversity using several drought-adaptive traits under rainfed conditions for two cropping seasons. Our results revealed that the ISSR primers produced 99 bands across the genotypes, the average of which was 6 fragments per primer, whereas CBDP primers generated 70 polymorphic bands, with an average of 5.3 fragments per primer. The values of marker index (MI) and polymorphism information content (PIC) indicated that CBDP markers were more efficient than ISSR markers for detection of genetic diversity in durum wheat. The average of PIC values for the CBDP and ISSR markers were 0.40 and 0.23, respectively. Based on the values of Shannon index (I) ICARDA population had a higher than CIMMYT population and the heterozygosis values confirmed these results. Dendrogram was created with a neighbor-joining clustering method. The studied genotypes were divided into five and seven groups based on data from the CBDP and ISSR markers, respectively, which was supported by principal coordinate analyses. The results of genotype by trait biplot analysis showed different patterns of interaction accessions and traits across years. High level of diversity among the studied accessions based on each studies trait was observed.

Evaluation of genetic diversity and DNA fingerprinting of 19 standard reference rice varieties using SSR markers

Molecular markers are advanced-tools for identifying new varieties at DNA levels. According to the International Union for the Protection of New Varieties ofPlants, new breeded varieties need to be tested for the Distinctness, Uniformity and Stability (DUS), before being recognized as the new ones. Traditional DUS criteria based on 62 - 65 morphological and biochemical characteristics, which evaluated on comparison of new varieties with 19 standard reference varieties for traits of interest. Study on the genotypic polymorphism of 19 standard reference rice varieties provides genotypic information of these varieties for the evaluation of new rice varieties based on genotyping analysis. The reference marker set (30 markers) was used to evaluate the genetic diversity and DNA fingerprinting of 19 standard reference rice varieties. The results showed the similarity coefficient of 19 varieties varied from 0.04 to 0.548. At the genetic similarity coefficient of 0.1, the 19 rice varieties divided into two main groups. Group one included 3 varieties: DH1, DH5, DH13. Group 2 included the remaining 16 varieties. Inside group two, phylogenetic tree divided into two main branches at the genetic similarity coefficient of 0.3. Branch 1 includes 5 varieties including DH2, DH6, DH10, DH11 and DH7. The 11 remaining varieties were in the branch 2. The most closely varieties were DH6 and DH10 with the genetic similarity coefficient of 0.548. This study shows that, the standard reference varieties have high uniformity and high genotypic polymorphism, could used for testing new varieties based on genotyping by DNA fingerprinting combining with phenotype.

Review on small ruminant conservation status and prospects in India.

Small ruminants always play a major role in the agricultural economy of India. They provide livelihoods to numerous small and marginal farmers. The diversity of small ruminant population is enormous in the country which contributes to agrarian economy. However, the genetic variety is now at risk due to indiscriminate cross-breeding, and change is farmer's preference towards high-producing breeds. The population statistics is showing a declining trend for the past several years. During time of climate change and outbreak of novel diseases, this genetic diversity is important as consumer preferences and climate is bound to change in future. So to ensure fitness and vitality in future populations of food-producing animals, and to keep genetic options open, access to greater diversity of genetic material will always be required. The native breeds of the country also possess several characteristics of disease tolerance, high fecundity and specific products which make them unique in their own aspect. Hence, conservation programmes should be adopted to maintain this large diversity of small ruminants. It may involve tradition practices followed by pastoralists or modern reproductive technologies like MOET. The government has taken several steps towards conservation and national institutes like NBAGR works for evaluation and conservation of native genetic diversity. However, better awareness among famers and improving of conservational approaches will go a long way in sustainable management of sheep and goat genetic resources.

Genetic diversity in Iranian indigenous sheep vis-à-vis selected exogenous sheep breeds and wild mouflon.

The heterogeneity of climate and different agro-ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari (n=37), Moghani (n=34), Qezel (n=35), Zel (n=46) and Lori-Bakhtiari (n=46), and Asiatic mouflon (n=8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds - Arabi (n=15), Balouchi (n=15) and Gadik (n=15); three indigenous breeds from Turkey and Cyprus - Cyprus Fat Tail (n=30), Karakas (n=18) and Norduz (n=20); and three commercial European breeds - Suffolk (n=19), Comisana (n=24) and Engadine Red Sheep (n=24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk (FROH =0.0544) and lowest for Balouchi (FROH =0.0078). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.

The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis

Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

Evaluation of Population Structure and Genetic Diversity of Cirrhinus mrigala among the Different Freshwater Rivers of Pakistan Using Molecular Marker: Study Implications and Its Importance in Aquaculture

Cirrhinus mrigala (Family Cyprinidae) have vast presence in different studied rivers of Pakistan. Present study was designed to formulate the genetic diversity of desired sites in Cirrhinus mrigala populations using nine Random amplified polymorphic DNA markers. Total hundred individuals were used to conduct this study and were collected from three distinct rivers (River Indus, Chenab and Ravi) with four specified sites with wild of Pakistan were used to study. A random Amplified Polymorphic DNA primer analyzes various bands of polymorphic loci. Mean genetic diversity within and between populations found 81.53% and 2.27% respectively by using analysis of molecular variance. Fixation index was found variably and Pairwise Fst analysis showed significant difference between different sites of studied populations. Genetic divergence information would mark essential in order to improve genetic programming its management and conservation of natural inhabitation. In order to quantify the study of population divergence by using these molecular markers is an efficient way to pin point the genetic diversity within and among population.

Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae).

Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.

Genetic diversity, admixture and the effect of inbreeding on milk performance in two autochthonous goat breeds

For the development of an appropriate program for the conservation of animal genetic resources, careful evaluation of the current genetic diversity in endangered breeds was performed. Pedigree data from a total of 38,288 animals registered in studbooks between 1970 and 2017 from two autochthonous Czech goat breeds, White and Brown Shorthair goats, were analysed to identify factors that may have affected the genetic variability of the breeds. Because the populations of both breeds are closed, there is concern about the loss of genetic variation. The average numbers of equivalent complete generations were 10 and 11 for White Shorthair goat and Bowen Shorthair goat, respectively. The effective numbers of founders contributing to the current genetic pool were 323 and 45, and the effective numbers of ancestors were 90 and 24, respectively. The average inbreeding and relatedness coefficients for the reference populations of the two breeds were 2% and 5.3%, respectively, for White Shorthair goats and 3.7 and 11.5% for Brown Shorthair goats. The corresponding estimates of the effective population size based on an increase in inbreeding or coancestry were 244 and 311, respectively, for White Shorthair goats and 82 and 87 for Brown Shorthair goats. Three kinds of inbreeding coefficients, the classical inbreeding coefficient, the new inbreeding coefficient and the ancestral inbreeding coefficient, were used to quantify the effects of inbreeding and purging on milk production in both analysed breeds. All tested inbreeding coefficients (FX, Fnew) showed a significantly negative influence on milk performance in the White Shorthair goat breed. The purging effect was confirmed based on the difference between FX and Fnew in White Shorthair goats and on the suitability of the statistical model in Brown Shorthair goats. These statistics suggest that genetic variability has decreased and inbreeding depression has occurred and that without changes in the breeding strategy, genetic variability might continue to decline.