Average Number Of Alleles Research Articles

Determining the genetic and agronomic variations in lines from Samsun tobacco growing areas

Tobaccos grown in Samsun are known all over the world. Samsun tobaccos are grown using nonregistered populations traditionally maintained by local farmers. The present study was conducted to determine the genetic and agronomic variations in Samsun tobaccos. Fifty-eight lines were collected from Samsun in tobacco growing area. These lines were analyzed using eighteen SSR markers. Polymorphic information content (PIC) values of markers ranged between 0.0 and 0.702. Forty-two alleles were obtained from 18 SSR markers. Average number of alleles per SSR locus was 2.33. Forty-eight lines were different for at least one SSR locus, indicating a high level of variation. The forty-eight lines were evaluated in two field trials along with local varieties Nail and Canik for agronomic characteristics such as plant height, number of leaves, leaf width, leaf length, leaf yield, grade index, leaf sugar and nicotine contents. High level of variation was also evident for agronomic characters. Lines No: 2, 11, 13, 21, 28 and 41 were notable for their superior agronomic characteristics. Some of these lines could be directly registered as new cultivars, but they should be further evaluated in future field trials in multiple environments. These lines could also be used as parents for the development of new cultivars.

Application of a custom haplotype caller to analyze sequence-based data of 56 microhaplotypes

Microhaplotypes (microhaps) are recently introduced markers that aim to complement the limitations of conventional forensic markers such as short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). With the potential of microhaps in forensics becoming clearer through massively parallel sequencing (MPS), MPS-based studies on microhaps are being actively reported. However, simpler workflow schemes for the generation and analysis of MPS data are still required to facilitate the practical application of MPS in forensics. In this study, we developed an in-house MPS panel that simultaneously amplifies 56 microhaps and a custom haplotype caller, Visual Microhap. The developed tool works on a web browser and provides four analysis options to extract SNP-based haplotypes from sequence-based data obtained by STRait Razor 3.0. To demonstrate the utility of the MPS panel and data analysis workflow scheme, we also analyzed 56 microhaps of 286 samples from four populations (African-American, Caucasian, Hispanic, and Korean). The average effective number of alleles (Ae) for the four groups was 3.45, ranging from 1.74 to 6.98. Forensic statistical parameters showed that this microhap panel is more powerful than conventional autosomal STRs for human identification. Meanwhile, the 56-plex panel mostly comprised microhaps with high Ae; however, the four populations were grossly distinguishable from each other by cluster analysis. Consequently, the developed in-house MPS panel for 56 microhaps and the adopted workflow using open-source tools can increase the utility of microhap MPS in forensic research and practice.

An overview of the diversity of Asian Elephants in Indonesia in Terms of Their Genetics

There are two species diversity of Asian elephants in Indonesia, namely: Sumatran elephant (Elephas maximus sumatranus) and Borneo elephant (Elephas maximus borneensis). This literature study aims to identify and analyze the diversity of Asian elephants in Indonesia, namely: Sumatran elephants (Elephas maximus sumatranus) and Borneo elephants (Elephas maximus borneensis) as seen from their genetics (Microsatellites). This elephant is listed in the red list book of the International Union for Conservation of Nature (IUCN) from precarious to critically endangered. Meanwhile, the Borneo Elephant (Elephas maximus borneensis) is included in the IUCN red list with the endangered category. The Amely gene of the Sumatran elephant's Y chromosome is used to trace offspring paternally. Meanwhile, Borneo elephants have low genetic diversity due to the low average number of alleles and heterezygotes and genetic research on Borneo elephants is also still small. For this reason, it is necessary to make further conservation efforts to maintain the Borneo elephant species that have unique characteristics. This Borneo elephant is a unique species, because it is smaller or dwarf in size than other elephants, with straight tusks and has a long tail

Genetic variability of mass-selected and wild populations of Iwagaki oyster (Crassostrea nippona) revealed by microsatellites and mitochondrial COI sequences

Crassostrea nippona has recently been identified as a potential aquaculture species for its high glycogen content and delicate flavor in summer when Crassostrea gigas suffer from low meat quality. In 2014, we initiated the selective breeding program to improve growth traits of C. nippona through successive generations of mass selection, yet the genetic impact of an intense artificial selection on the genetic variability of C. nippona was not fully understood. In this study, the genetic diversity and genetic structure of three generations of mass-selected lines (G1-G3) and three wild populations were investigated using both 15 microsatellite loci and mitochondrial COI sequences (mtCOI). The selected lines exhibited no significant decrease in the average number of alleles (Na: 7.53–9.87), observed heterozygosity (Ho: 0.58–0.64), expected heterozygosity (He: 0.67–0.71) and alleles richness (Ar: 6.35–7.75), compared with those of the wild populations. The abundant genetic diversity of selected lines was successfully maintained during three generations of mass selection due to no detectable loss. The effective population sizes (Ne−lin) estimated by linkage disequilibrium methods for G1, G2 and G3 were 64.1, 25.3 and 47.4, respectively. Moreover, little genetic differentiation within the selected lines was observed in AMOVA analysis (global FST: 0.005, P > 0.05) and significant genetic differentiation among the wild populations was revealed by global FST (0.15, P < 0.01), pairwise FST (0.095–0.211), Nei's D (0.260–0.730) and clustering results, which might suggest genetically isolated populations occurring in these sampling locations. To maximize future selective breeding efforts, a larger scale of broodstock and multi-line breeding strategy along with alleviating selection intensity is recommended against the reduction in the genetic diversity and effective population size in subsequent breeding practices. This study contributes to an increasing understanding of the efficiency of current breeding procedures in maintaining genetic variation and provides insight into future genetic improvement programs of C. nippona.

A Study of Genetic Variability 30 Rice Genotypes (Oryza sativa L.) Using Some SSR (Simple Sequence Repeat) Markers Adrift Zn

Rice is one of the important commodities in indonesia. Analysis of rice genetic diversity is necesarry for the succes of the local rice variety program. This study aims to identify the genetic variability and kinship patterns of 30 rice genotypes (Oryza sativa L.) using six zinc-linked SSR (Simple Sequence Repeat) markers. The research was conducted in September - December 2021 at the DNA Laboratory of the Sukamandi Rice Plant Research Center. A total of 30 local rice genotypes with diverse Zinc content have been analyzed using laboratory experiments. The results showed that there were different allele variations (2 – 8) among the genotypes tested with an average number of alleles of 4.5, while the average value of Polymorphism Information Content (PIC) amounted to 0.48 (0.20 - 0.70). 4 SSR markers have PIC values of &gt; 0.5 (RM162, RM38, RM30, and RM80) which show that the markers are informative for the study of rice genetic diversity with Zinc content variety with an average gene diversity value of 0.53. The results of the phylogenetic analysis showed that the 30 genotypes clustered into five clusters with a similar coefficient of 0.68.

SSR marker-based genetic characterization of Turkish oriental tobaccos.

Turkey is one of the traditional oriental tobacco producing countries. Oriental tobaccos produced in Turkey are ecotypes specific to certain regions, local varieties and landraces, and they have unique characteristics. The present study was conducted to reveal the general and interregional genetic diversity levels of tobacco genotypes collected from different regions of Turkey based on DNA markers. A total of 319 ecotypes/lines of Turkish Oriental Tobaccos collected from different regions (Aegean Region, Marmara Region, Karadeniz Region, and East and Southeast Anatolia Regions) of Turkey and cultivars Xanthi 81, Xanthi 2A, Canik Sitmasuyu, Katerini, Canik 190-5 and NC 55 were subjected to SSR marker analysis. Eighty-nine alleles were obtained from 21 markers examined, and the average number of alleles per marker was 4.05. A total of 314 unique tobacco genotypes were found among 319 plants evaluated using 19 polymorphic SSR markers. In the dendrogram constructed using SSR marker data, genotypes were divided into six clades based on geographic regions and levels of genetic diversity. The presence of 314 unique genotypes among 319 tobacco plants evaluated indicated the high level of genetic diversity among Turkish tobaccos. While some of them were N. rustica tobaccos, some others were reminiscent of semi-oriental tobaccos. These genotypes merit further agronomic and technological characterizations, which could allow their utilization in future tobacco breeding.

Exploring genetic diversity and Population structure of five Aegilops species with inter-primer binding site (iPBS) markers.

Turkey is not only a center of origin for wheat, but also contains wild forms of various cereals. Turkey, located in the Fertile Crescent, has conserved its genetic richness to the present day. The aim of the study was to investigate the genetic diversity of 70 wild wheat species, to evaluate the structure of diversity in germplasm and to generate useful data for further breeding programs. Genetic diversity and population structure of 70 wild wheat species (Ae. cylindrica, Ae. geniculata, Ae. triuncialis, T. dicocoides, Ae. columnaris) collected from Eastern and Southeastern Anatolia regions of Turkey were investigated in this study with the use of inter-primer binding site (iPBS) markers. Of 35 iPBS primers used, 11 yielded a total of 61 alleles. Number of alleles per marker varied between 2 (iPBS-2085) and 9 (iPBS-2394) with an average value of 5.55. Polymorphic information content (PIC) values varied between 0.22 and 0.47, with an average value of 0.35. Average number of effective alleles (Ne) was identified as 1.9488, Nei's genetic diversity (H) as 0,4861 and Shannon's information index (I) as 0.6791. Cluster analysis through unweighted pair-group mean average (UPGMA) method revealed that 70 wild wheats were divided into three main clusters. Genetic similarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 19% (YB2 and YB70) and 98% (YB66 and YB67). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 62.33% of total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2666 (the first sub-population) and 0.2330 (third sub-population), with an average value of 0.2500. Average population differentiation measurement (Fst) was identified as 0.3716 for the first sub-population, 0.3930 for the second subpopulation and 0.4804 for the third sub-population. Based on present findings population structure of 70 wild wheat genotypes collected from Eastern and Southeastern Anatolia regions of Turkey were successfully characterized with the use of iPBS markers. Present findings suggested that iPBS-retrotransposon markers could reliably be used to elucidate genetic diversity of Aegilops genotypes.

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers.

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.

SCoT markers assisted evaluation of genetic diversity in new plant type (npt) lines of rice

Rice being a stable food crop has wide range of diversity and distribution throughout the globe. Recently in hybrid rice breeding program new plant types have been developed through line x tester mating with the use of male sterility system. Genetic diversity and insight amplification among 43 New Plant Type (NTP) lines of rice using 15 start codon targeted polymorphism markers were tested. Out of 25 start codon targeted polymorphism (SCoT) primers, only 15 SCoT primers were amplified and produced 76 alleles with 83.26 per cent polymorphism. Average number of alleles per primer was 5.06, while polymorphism information content ranged from 0.28 to 0.67 with an average of 0.50 per primer. Dandogram cluster falls in two major group having 31 and 12 NPT lines respectively. Bangladesh J. Bot. 51(2): 335-341, 2022 (June)

Development of microsatellite DNA markers for Indian Rat snake (Ptyas mucosa)

Thirteen microsatellite markers were developed for one of the vulnerable snake species Indian Rat snake (Ptyas mucosa) in Indian ecosystems that are now subject to much restoration efforts. All loci were polymorphic when tested across 25 individuals. The average number of alleles per locus varied from 4 to 7 (mean 5.2). Observed and expected heterozygosity ranged from 0.76 to 1.00 and 0.59–0.94, respectively and the average polymorphic information content is 0.664 were identified demonstrating the utility of these markers for the investigation of the population genetic structure and diversity of this species.

Use of SSR Markers for the Exploration of Genetic Diversity and DNA Finger-Printing in Early-Maturing Upland Cotton (Gossypium hirsutum L.) for Future Breeding Program

DNA fingerprinting and genetic diversity analysis of 79 early-maturing upland cotton (Gossypium hirsutum L.) cultivars were performed using Simple Sequence Repeat (SSR) molecular markers. Out of 126 pairs of SSR primers, we selected 71 pairs that gave good polymorphisms and clear bands, had good stability, and showed even distribution on the cotton chromosomes, and 142 polymorphic genotypes were amplified. The average number of alleles amplified with the SSR primers was 2.01. The polymorphism information content (PIC) of the markers ranged from 0.1841 to 0.9043, with an average of 0.6494. The results of fingerprint analysis showed that nine varieties had characteristic bands, and at least six primer pairs could be used to completely distinguish all 79 cotton accessions. Using NTSYS-pc 2.11 cluster analysis, the genetic similarity coefficients between the cotton genotypes ranged from 0.3310 to 0.8705, with an average of 0.5861. All cotton accessions were grouped into five categories at a similarity coefficient of 0.57, which was consistent with the pedigree sources. At the same time, the average genetic similarity coefficients of early-maturing upland cotton varieties in China showed a low-high-low pattern of variation over time, revealing the development history of early-maturing upland cotton varieties from the 1980s to the present. This also indirectly reflects that in recent years, China’s cotton breeders have focused on innovation and have continuously broadened the genetic resources for early-maturing upland cotton.

Genetic diversity analysis of Camellia fascicularis H. T. Chang based on SSR markers

Camellia fascicularis is a Camellia specie with extremely small populations and unique to Yunnan Province. This study aimed to analyze the genetic diversity of C. fascicularis populations using polymorphic SSR markers. Eighty four samples of eight natural populations were tested for genetic diversity using fourteen SSR markers. The numbers of alleles detected at single polymorphic loci using 14 SSR markers were 2–8, and a total of 68 alleles were identified in this study, with an average allele number of 4.8571 per locus. The average Shannon’s information index I was 1.0925, indicating that C. fascicularis has a high diversity. The percentages of polymorphic loci (PPB) of the eight populations of C. fascicularis were 42.86 %−100 %. There were significant differences in genetic parameters among different populations, and the polymorphisms were all high. The gene flow (Nm) values ranged from 0.0503 to 0.9820, with an average value of 0.5440 < 1. Genetic structure analysis showed that the eight C. fascicularis populations were roughly divided into three groups. Genetic variation occurred mainly within populations, with intra-populations genetic variation accounting for 49.95 % of the total variation. It was found that C. fascicularis has a high genetic diversity, and its rich genetic diversity may be due to the diverse habitat diversity of its distribution area and the long evolutionary history of the species. There was almost no gene exchange among natural populations, and the level of population differentiation was low.

Analysis of Population Genetic Diversity and Genetic Structure of Schizothorax biddulphi Based on 20 Newly Developed SSR Markers

To protect the germplasm resources of Schizothorax biddulphi, we developed and used 20 pairs of polymorphic microsatellite primers to analyze the genetic diversity and structure of populations. A total of 126 samples were collected from the Qarqan River (CEC), Kizil River (KZL), and Aksu River (AKS) in Xinjiang, China. The results showed that 380 alleles were detected in 20 pairs of primers and the average number of alleles was 19.0. The effective allele numbers and Nei’s gene diversity ranged from 1.1499 to 1.1630 and 0.0962 to 0.1136, respectively. The Shannon index range suggested low levels of genetic diversity in all populations. The genetic distance between the CEC and AKS populations was the largest, and the genetic similarity was the smallest. There was a significant genetic differentiation between CEC and the other two populations. The UPGMA clustering tree was constructed based on population genetic distance, and the clustering tree constructed by individuals showed that the AKS population and KZL population were clustered together, and the CEC population was clustered separately. Also, the group structure analysis also got the same result. It can be seen that although the three populations of S. biddulphi do not have high genetic diversity, the differentiation between the populations was high and the gene flow was limited, especially the differentiation between the CEC population and the other two populations. This study not only provided genetic markers for the research of S. biddulphi but the results of this study also suggested the need for enhanced management of S. biddulphi populations.

Genetic characterization of cultivated apple (Malus x domestica Borkh.) in Morocco using microsatellite (SSR) markers

Genetic diversity of 27 apple genotypes from four geographical regions of Morocco was analyzed using 26 simple sequence repeat (SSR) primers. In total, 195 polymorphic SSR alleles were detected, with sizes ranging from 78 to 209 bp. The results obtained for the average number of alleles per locus (7.5), effective number of alleles (4.62), Shannon information index (1.66), expected heterozygosity (0.76), observed heterozygosity (0.74) and polymorphism information content (0.76) showed a moderate level of polymorphism, which suggests that Moroccan apple cultivars exhibit significant genetic diversity. Over the 26 SSR loci used, the probability of identity P (ID) was 4.62 10 −29 indicating that most markers were highly discriminating and powerful for cultivars characterization. The principal coordinate analysis and hierarchical classification suggested the presence of four well defined groups, which was confirmed later by model based population structure. Furthermore, strong genetic differentiation between these four groups was also detected (FST = 0.28) . Most of the individuals segregated into the four groups showing a membership coefficient greater than 0.80, which indicates their better genetic integrity. A parentage analysis, however, shows that cultivars from the four regions are minimally hybridized. After comparing SSR profiles and genotypes names, we conclude that the problem of homonyms and/or labeling errors appear in the studied cultivars.Thus, based on genetic profiles, two individuals (Beldi 1/Beldi 2 and Laakri 5/Laakri 6) found to be duplicated. Additionally, some cultivars with the same name are grouped in different clusters suggesting the existence of possible homonymy. Lastly, the present work confirms the usefulness of SSR markers for the elimination of duplications and characterization of diversity and hybrid characters of apple genotypes in Morocco.

Genetic Structure and Demographic History of Yellow Grouper (Epinephelus awoara) from the Coast of Southeastern Mainland China, Inferred by Mitochondrial, Nuclear and Microsatellite DNA Markers

The yellow grouper (Epinephelus awoara) is distributed in the West Pacific Ocean. Its genetic structure and demography were investigated using mitochondrial COI, Cyt b, the ND2 gene, the nuclear RyR3 gene, and 10 microsatellite DNA markers. A total of 120 individuals were collected from four locations along the coast of southeastern mainland China. High levels of haplotype diversity (0.968) were observed in mitochondrial DNA, and the average number of alleles ranged from 13.4 to 20.3 in microsatellite DNA data, which showed that all populations exhibited a high level of genetic diversity. Deficiency of heterozygosity was observed in all populations with positive FIS, showing that the characteristics of hermaphroditism might also be an underlying cause. The results of PCA, UPGMA clustering analysis and the significant genetic differentiation found in the Beibu Gulf population revealed the prevention of gene flow caused by the Qiongzhou Strait. The population of E. awoara also presented two major lineages, resulting in the appearance of the land bridge of the Taiwan Strait as a possible factor during the Pleistocene glaciation. Analysis of demographic history revealed that E. awoara underwent a reduction in effective population size in the past, followed by a single instantaneous increase in population size.

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers.

Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (NA), expected heterozygosity (HE), and Shannon’s information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (Nm = 1.252) and high genetic differentiation (Fst = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.

Evaluation of the Current State of Preservation of Vaccinio uliginosi-Pinetum Kleist 1929 in Eastern Poland

The study assessed the genetic variability and the possibility of Scots pine regeneration in marshy forest. The genetic parameters were determined using the ISSR technique. The relationships between herbaceous plants, pine regeneration density, and their genetic variability were determined. On average, per 1 m2, three regenerated pine seedlings with a mean height of 27.56 cm were inventoried. Based on genetic analysis, it was found that the proportion of polymorphic loci was 60.46%. The average number of alleles at the locus was 1.345, and the effective number of alleles at the locus was 1.345. The values of the expected heterozygosity and Shannon index were 0.200 and 0.301, respectively. No species competing with pine regeneration were found. A significantly negative correlation of the number of pine regenerations with the area covered with an herbaceous plant layer and tree canopy closure was found. There was a relation to the insufficient amount of light under the stand canopy. In conclusion, the condition of marshy forests was satisfactory and the genetic variability of pine seedlings was moderate. The vegetation was typical for this habitat, but the significant presence of dry habitat species could indicate the beginning of habitat drainage. It seemed that the amount of light under the stand canopy was insufficient. Nevertheless, more light probably reached the inside of the stand in the terminal stage, as a result of upper layer tree separation, which in turn may facilitate the effective regeneration of Scots pine in this habitat.

Genetic diversity and population structure of Dermatophagoides farinae based on microsatellite markers

ABSTRACT Dermatophagoides farinae is one of the most important allergens that cause allergic diseases and trigger serious harm to the human body. D.farinae is widely distributed, and the development of genetic markers and genetic information regarding the populations of this species are needed to establish control strategies. The aim is to develop a microsatellite marker and assess the genetic diversity and population structure of different populations of D. farinae. The genomic DNA of D. farinae was extracted and sequenced by NGS analysis. Microsatellite markers were identified and screened with MISA software. Primers were designed with Primer5.0 and screened by capillary electrophoresis detection. Genotyping was implemented with GeneMarker 2.2. Genetic diversity and population structure were analysed by related softwares. Twelve microsatellite markers detected 66 alleles in 256 individuals of D. farinae from 12 geographic populations. The average allele number (Na), effective allele number (Ne), observed heterozygosity (Ho), and expected heterozygosity (He) were 4.431, 2.610, 1.056 and 0.484, respectively. Genetic variation existed within populations and there was no correlation between geographic distance and genetic distance (Fst) (P = 0.160). Structure analysis showed D. farinae is largely divided into three groups. The genetic diversity of the geographical population of D. farinae is relatively high.

Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China.

Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of L. yunnanensis has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of L. yunnanensis was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of L. yunnanensis. The results showed that 98,389 unigenes were obtained from the L. yunnanensis flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for L. yunnanensis.

Morphometric characteristics and microsatellite markers based diversity and differentiation recognizes the first prospective cattle breed from the Jharkhand state of India

India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (>0.6) and the average number of alleles per locus (>8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei’s genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8–7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households.