Phenotypic and Genetic Diversity Evaluation of Sengon (Falcataria moluccana (Miq.) Barneby & JW Grimes) from Solomon Provenance on Progeny Trial in Cirangsad Experimental Forest, West Java

Initial evaluation of phenotypic variability and genetic diversity was conducted on the progeny test of 2 years-old sengon from Solomon provenance, which derived from nine families of mother tree and were then planted in 4 blocks in the Cirangsad Experimental Forest. Phenotypic assessment on eight traits was conducted on 36 trees using a scoring system, while genetic diversity of 15 selected individuals which represented high and low-score phenotypic traits was analyzed using 5 selected RAPD primers. The result on phenotypic assessment showed that family 3 (57.25 points) has the highest average score of phenotypic quality and family 4 has the lowest average score (7.50 points). Furthermore, genetic analysis showed that the low-scoring sengon population had a greater mean genetic diversity (He = 0.2535) than the high-score population (He = 0.2345). The analysis of molecular variance (AMOVA) revealed a significant genetic differences (p-value < 0.001) among high and low-score populations and the dendrogram of genetic distance revealed clustering of individuals having similar superior phenotypic against those having non-superior, indicating the selection based on phenotypes in this study had succeeded in pooling the good quantitative alleles in the selected population. This evaluation results can be used as a reference in determining the best families to produce superior sengon (from Solomon provenance) offspring in the future that have desired adaptability, productivity, and diversity.

Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

Genetic Profiling of Sida rhombifolia Originated from Several Indonesian Ethnicities Based on Sequence-Related Amplified Polymorphism Markers

Sida rhombifolia is one of wild flowering plants that grows easily in many habitats with moderate humidity, with some usefulness in traditional medicine. Genetic characterization of Sida rhombifolia accessions originated from 12 ethnicities of Indonesia was analyzed based on Sequence-Related Amplified Polymorphism (SRAP) Markers. The genomic DNA were extracted from leaf samples and then were characterized by using the SRAP marker system according to Li and Quiros (2001). Nine pairs of SRAP primer resulted high polymorphic bands and were used in the genetic profiling. The data analysis was performed using GenAlEx to calculate genetic distance, Principal coordinate analysis, and Analysis of Molecular Variance (AMOVA), also using POPGENE to assess genetic diversity (Hs and Ht) and Nm to predict gene flow among populations. The coordinate analysis showed that the accessions originated from ethnicities along Wallacean line tend to differ genetically from most other locations. However, the results of analysis of molecular variance suggested that there were only slight differences (0.1%) found between ethnicities, while most genetic variances (99.9%) were found mostly among accessions within populations. The results suggested that there was an extensive genetic flow and plant spreading among Sida rhombifolia plant populations, resulting more homogenous genetic characters among most populations, while high diversity within population. The calculation of the number of migration (Nm = 1.7341) confirmed that the high rate of gene flow had occurred between populations.

Assessment of Genetic Diversity and Relationship of the Two Sanga Type Cattle of Botswana Based on Microsatellite Markers

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana; Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INTRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations; Tswana (He=0.7895±0.033 vs Ho=0.631±0.091) and Tuli (He=0.8123±0.033 vs Ho=0.556±0.021). The inbreeding coefficient was 0.200±0.002 and 0.332±0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding program is likely to result in minimal heterosis and therefore not recommended.

Population Genetic Structure and Phylogeography of Co-Distributed Pachymeniopsis Species (Rhodophyta) along the Coast of Korea and Japan

Inferring phylogeographic patterns of macroalgal species is essential for understanding the population structure and for the conservation of macroalgal species. In this study, the phylogeographic patterns of two co-distributed macroalgal species along the coast of Korea and Japan, Pachymeniopsis lanceolata and Pachymeniopsis elliptica, were analyzed. Pachymeniopsis lanceolata (215 specimens from 36 sites) and P. elliptica (138 specimens from 24 sites), using the plastid rbcL gene, are characterized by fifteen and six haplotypes, respectively. Mitochondrial COI-5P gene sequences revealed a low variation for both species. An analysis of molecular variance (AMOVA), pairwise FSTcomparisons, and haplotype networks based on the rbcL data suggest a weak genetic differentiation of both species. The shared haplotypes (P. lanceolata: LR01; P. elliptica: ER01) found in the entire sampling range indicate that these two Pachymeniopsis species can disperse over long distances along the coast of Korea and Japan. Despite the similar phylogeographic pattern, our results suggest that P. lanceolata has a higher genetic diversity, with a wider distribution along the Korean Peninsula than P. elliptica. Moreover, it is adapted to low sea surface temperatures and survived in more of the available habitats during periods of climatic change, whereas P. elliptica is less adaptable and more susceptible to environmental disturbance. This phylogeographic study provides a rationale for the conservation of the wild Pachymeniopsis population.

Genetic diversity and structure analysis of Croatian garlic collection assessed by SSR markers

This study examines genetic diversity and structure of a Croatian garlic germplasm collection using 13 simple sequence repeat (SSR) markers. A total of 71 alleles were observed across 64 accessions representing 3 Croatian regions (Istria, Dalmatia and continental Croatia) and 16 foreign landraces, with an average of 5.46 alleles per locus. Among the 80 accessions analysed, 61 distinct multilocus genotypes (MLG) were identified, of which 51 represented unique genotypes and the remaining accessions were divided into 10 MLG groups, comprising potential duplicates or redundant genotypes. Model-based Bayesian and hierarchical UPGMA clustering approaches revealed five major groups within the collection which partially correlated with geographical origin. The analysis of molecular variance (AMOVA) showed that the majority (87.71%) of the total molecular diversity is within the Croatian groups of accessions, even though a significant share (12.29%) of diversity derived from genetic diversity among groups. These results support regional structuring, as well as the existence of significant diversity within local populations. This study is the first comprehensive report on an extensive evaluation of genetic resources of garlic maintained by Croatia with the aim of setting the course for future preservation strategies with particular emphasis on the value of diversity in the context of climate change both on macro and micro levels.

Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Different approaches to using the analysis of molecular variance (AMOVA) to assess the genetic differentiation of populations have been compared in the research. Data on 11 microsatellite loci of 84 bulls of seven breeds were used. The results were compared for three options of the AMOVA module of the GenAlEx 6.502 program: the allele distance matrix (calculated FST(W&C)(=θ) statistics – variant AMOVA1); the genotype distance matrix (ΦPT– AMOVA2); and the allele size difference matrix (RST– AMOVA3). Similar summary estimates of the genetic differentiation of breeds were obtained: FST(W&C)= 0.108, ΦPT= 0.115, RST= 0.110 (all with pperm≤ 0.001). Between the estimates of FST(W&C)and ΦPTfor each locus, the correlation coefficient was 0.99 (pvalue<0.0001); no statistically significant correlations with RSTwere found. A high correlation of FST(W&C)and ΦPTwith the estimates of differentiation according to Nei’s (0.96) was found. Programs other than GenAlEx (Arlequin v.3.5, GenePop v.4.7.3, RST22) gave similar AMOVA estimates. The negative linear dependence of FST(W&C)and ΦPTon the level of the average heterozygosity of the breed samples was established (R2= 0.6, rS= -0.75 for pvalue < 0.02) and the absence of such dependence for RST(R2= 0.04, rS= -0.23 for pvalue= 0.47). The standardization of the FST(W&C)and ΦPTestimates according to Hedrick’s eliminated this dependence and raised the initial estimates to 0.35 and 0.37, respectively. The latter were comparable to the estimates obtained by the Nei-Hedrick’s (0.364-0.375), Jost’s (0.292), and Morisit-Horn’s (0.308) methods. The Mantel correlations between the matrices of paired genetic distances (GD) calculated by different measures were >0.9 in most cases. The projections of the GD matrices in the principal coordinate analysis (PCoA) on the 2D plane were generally similar. The PCoA identified a cluster of Holstein «ecotypes», a cluster of «Red» breeds, and a branch of the Jersey breed. In the two-factor AMOVA of data on clusters (as two «regions»), the interregional GD was 0.357; the differentiation of breeds within the «regions» did not exceed 0.027. Modeling the association of breeds with close to zero GD resulted in an increase in the number of alleles per locus in the «new» breeds by 29 %, and an increase in the combined estimate of genetic differentiation by 29-46 %. The results obtained can be used in the development of measures for the conservation of endangered breeds.

DNA intensity and genetic diversity of oil palm (Elaeis guineensis) to determine an elite low lipase line

Angkat NU, Siregar LAM, Basyuni M, Afandi D, Syahputra I. 2021. DNA intensity and genetic diversity of oil palm (Elaeis guineensis) to determine an elite low lipase line. Biodiversitas 22: 900-905. The acidification of palm oil due to lipase activity in the mesocarp is assessed under genetic control. Three molecular markers have been established to gauge the lipase gene in oil palm. Lower lipase activity is desired for good quality edible oil. This study aims to identify the genetic diversity by screening groups/families to determine an elite low lipase genotype of oil palm. Genetic diversity and population structure of 15 groups of oil palm were investigated by using three specific markers with GenAlex 6.502 software. Results show that the Polymorphic Informative Content (PIC) value of markers was around 0,985-0,993, which indicates that these markers are effective in determining the diversity of lipase activity in oil palm. Analysis of molecular variance (AMOVA) revealed that genetic diversity varies within individuals (54%), among individuals (31%), and among population (15%). The value of number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and number of allele migration (Nm) indicate that the genetic diversity in this population is relatively low. Phylogenetic analysis identified two main groups as high lipase and low lipase activity groups based on DNA intensity.

Genome-Wide Association Study of Actinidia Chinensis

Background: A total of 74,936 SNPs were employed to carry out GWAS and post-GWAS of the fifty-six accessions, representing the two most valuable varieties of Actinidia chinensis, namely, A. chinensis var. chinensis and A. chinensis var. deliciosa, are mainly distributed in China. The percentage of heterozygous sites of A. chinensis var. deliciosa is higher than that of A. chinensis var. chinensis, which could be one of the reasons for A. chinensis var. deliciosa high disease resistance. LD decay distance of male plants is shorter than that of female plants. Results: Fifty-six accessions were divided into two subgroups. Analysis of molecular variance shows that the frequency of genetic variations within the population is 83.53% and 16.47% between populations. Fst between the two populations is 0.14, and Nm is 1.60. Set at α ≤ 0.05, a total of 327 SNPs and 260 haplotypes were related to the hispidus. A total of 246 proteins were annotated using GO and KEGG analyses, which indicated the membrane-related genes and stress-resistant metabolic pathways are related to the hispidus condition of leaves, stems, and peels of kiwifruit, which is also the result of the adaptation of A. chinensis var. deliciosa to its growth environment. Conclusions: Haplotype analysis showed that the evolution of is A. chinensis var. deliciosa later than that of A. chinensis var. chinensis.

Genetic variation of the major histocompatibilty complex-B haplotypes in Nigerian local chicken populations

To understand the genetic basis and mechanism underlying the differences in the level of immunity among and within chicken populations in Nigeria, it is important to start from the Major Histocompability Complex (MHC) region particularly as it serves as a reservoir for genes of the immune system. The B-complex of chicken major histocompatibility complex, located on microchromosome 16, consists of gene classes responsible for immunity through antigen presentation to T cells. A highly polymorphic tandem repeat marker (LEI0258) located within the B-complex has been a marker of choice for genotyping to identify major histocompatibility complex-B haplotypes and to study the genetic diversity of chicken populations. This study was carried out to determine the genetic variations, at the LEI0258 locus, in three Nigerian local chicken populations; Normal feather, Frizzle feather and Naked neck. The allelic and genotypic profiles of each representative from each population were determined through polymerase chain reaction amplification of the repeat region. The genetic diversity parameters, analysis of molecular variance and evolutionary relationship were determined using GenAlex, FSTAT, Arlequin and POPTREEW, respectively. 76 % of the entire population was heterozygous at the LEI0258 locus. Analysis of molecular variance revealed that large proportion of the total variations across populations was due to variation between individuals (79 %), whereas variations among the populations and among individuals within populations only accounted for less than 1 % and 21 %, respectively. Using Anak Titan as an exotic outgroup, the evolutionary relationship among the Nigerian local chicken populations was studied and a Nei-based dendrogram showed two major clades separating the exotic population from the Nigerian local chicken populations. The identified diversity at the locus could be exploited for usage in further breeding programmes especially for disease resistance and fitness in locally adapted chicken populations in Nigerian.