GENETIC PERFORMANCE OF THE STRIPED CATFISH (Pangasianodon hypophthalmus Sauvage, 1878) POPULATION DERIVED FROM SELECTIVE BREEDING

Selective breeding to improve growth trait in striped catfish (Pangasianodon hypophthalmus) need genetic performance data. This study was carried out to evaluate genetic performance of different generations of the striped catfish population derived from selective breeding. Fifty fish of each population from four generations selected striped catfish was analyzed using five microsatellite loci (Pg-1, Pg-2, Pg-3, Pg-13, and Pg-14). Microsatellite allele data were analyzed using Microsoft Excel, Arlequin, and Fstat software. A neighborhood joining dendrogram was constructed based on Nei’s distance (Da) matrix with 1,000 bootstrap replications using MEGA7 software. The result showed that totally 31.5 exist, ranged from 4-7. Number of allele was ranged from 5.0 to 5.2, and polymorphic data was from 0.45-0.60. There were some exception, such as the allele of the loci Pg-2—194 bp, Pg-13—227 bp, Pg-13—229 bp, and Pg-14—279 bp; their gene frequencies were increased by generation. Further analyses indi­cated that most genetic variations arise from individuals within populations (approximately 57.10%). The founder generation closely related to G-0 generation. Likewise, G-1 generation closely related to G-2 generation. This result indicated that selection activity had a very significant impact on the genetic improvement of the selected population.

Population genetics and ecology of Sumatran camphor (Dryobalanops aromatica) in natural and community-owned forests in Indonesia

Ritonga FN, Dwiyanti FG, Kusmana C, Siregar UJ, Siregar IZ. 2018. Population genetics and ecology of Sumatran camphor (Dryobalanops aromatica) in natural and community-owned forests in Indonesia. Biodiversitas 19: 2175-2182. Dryobalanops aromatica Gaertn. f. (Sumatran camphor) is a valuable tree species that produces borneol (camphor) and good-quality timber. However, the population of this species has declined due to illegal logging and conversion of forests into plantations and has been classified as Critically Endangered by the International Union for Conservation of Nature. This study aimed to examine the genetic variation and spatial distribution of this species in a community-owned forest (Barus) and two natural forests (Singkohor and Danau Paris) in Indonesia using the Random Amplified Polymorphic DNA marker. The results of this study showed that D. aromatica had moderate levels of genetic variation (expected heterozygosity [He] = 0.1760 [Barus population] to 0.2134 [Singkohor population]) and genetic differentiation (Nei’s Gst = 0.1257). The genetic distance was the smallest between the Singkohor and Danau Paris populations (Nei’s distance = 0.0363) and greatest between the Singkohor and Barus populations (Nei’s distance = 0.0534). The spatial distribution of D. aromatica was grouped in both Barus and Danau Paris based on Morisita’s index of diversity (ip = 0.06 and 0.043, respectively). These findings indicated that genetic conservation might be performed in situ in combination with enrichment planting using locally propagated sources.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

Diversidad genética y relaciones filogenéticas del ganado criollo colombiano

<p>La caracterización genética del ganado criollo colombiano (gcc) ha demostrado el valor de estas razas en los sistemas productivos tropicales, lo que ha despertado el interés para desarrollar programas de conservación y multiplicación. Se adelantó un estudio de análisis genético con las siete razas de ganado criollo colombiano, (rgcc): Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) y Casanareño (Ca), utilizando el Cebú (C) como control, con el objeto de evaluar su diversidad genética y relaciones filogenéticas. Se usaron 7 microsatélites (STR) para establecer las distancias genéticas amplificadas mediante PCR. El tamaño de los loci se definió mediante marcaje con ɣ³² P seguido de un pase en geles de poliacrilamida (PAGE) o marcados con fluorescencia y electroforesis capilar. Los datos se analizaron usando los programas Genepop, GDA y Phylip. El número promedio de alelos por locus fue de 8,9 y Ia heterocigosidad promedia observada fue de o,52. El árbol filogenético construido con el programa Phylip, empleando la distancia de Nei y el algoritmo de Neighbour-joining, agrupó en dos las gcc. En el grupo uno las razas: BON, SM, R, CCC y H; y en el grupo dos las razas: Ch, Ca y C. Los resultados de evaluación filogenética de las gcc indicaron que existe diversidad genética adecuada en estas razas para programas de mejoramiento genético; sin embargo, se recomienda continuar el estudio con un mayor número de marcadores genéticos.</p><p><strong><br /></strong></p><p><strong>Diversity and Phylogenetic Relations of Colombian Criollo Cattle.</strong></p><p>Studies of genetic characterisation of Colombian criollo cattle (gcc) has shown the value of these breeds in tropical production systems; consequently attention is noticeably growing to develop conservation and multiplication programs. A genetic analysis study was conducted including the seven criollo cattle breeds: Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) and Casanareño (C), using Cebu as external control breed, with the purpose to evaluate genetic diversity and philogenetic relations. Seven microsatellite (STR) were used to detect length variations amplified by the PCR and sized by means of ɣ³² P, runned in PAGE or tagged with a fluorescent dye and electrophoresis. Data were analysed using Genepop, GDA and Phylip programs. Mean number of alleles by loci were 8.9 and mean heterozygocity was o.52. The phylogenetic tree developed using Phylip program, the Nei's distance and the neighbour-joining aglorithm grouped in two the gcc. Group one included: Bon, SM, R,CCC and H, and the second group included Ch, Ca, C. Results of the phylogenetic relations of gcc showed that these breeds have adequate genetic diversity for breeding Programs; however we suggest to carry out studies including higher number of genetic markers.</p>

050 Comparative Analysis of Cultivated Melon Groups (Cucumis melo L.) using Random Amplified Polymorphic DNA and Simple Sequence Repeat Markers

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to characterize genetic relationships among 46 accessions in two C. melo L. subsp. melo (Cantalupensis, Inodorus) and subsp. agrestis (Conomon and Flexuosus) groups. Genetic distance (GD) estimates were made among and between accessions in four melon market classes [Galia, Ogen, Charentais, and Shipper (European and U.S. types)] of Cantalupensis, one market class of Inodorus (Cassaba and Honey Dew), one accession of Conomon, and one accession of Flexuosus by employing three GD estimators; simple matching coefficient, Jaccard's coefficient, and Nei's distance-D. Differences detected among 135 RAPD bands and 54 SSR bands (products of 17 SSR primers) were used to calculate GD. Band polymorphisms observed with 21 RAPD primers and 7 SSR primers was important in the detection of genetic differences. Estimators of GD were highly correlated (P > 0.0001; rs = 0.64 to 0.99) when comparisons were made between estimation methods within a particular marker system. Lower correlations (P > 0.001; rs = 0.17 to 0.40) were detected between marker systems using any one estimator. The GD of the Conomon and Flexuosus accessions was significantly different from the mean GD of all the market classes examined, and market classes were distinguishable from each other. Although lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs, the genetic relationships identified using these markers were generally similar. Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined.

Using Isozyme Polymorphisms for Identifying and Assessing Genetic Variation in Cultivated Pawpaw [Asimina triloba (L.) Dunal]

The utility of isozyme phenotypes for identifying and determining genetic variation in pawpaw cultivars was studied using isoelectric focusing in thin-layer polyacrylamide gels. Based on a sample of 32 clones (cultivars and advanced selections) and 23 enzyme systems, 7 enzymes were found to be polymorphic, involving 9 polymorphic loci [acid phosphatase (ACP), dihydrolipoamide dehydrogenase (DDH), malic enzyme (ME), phosphoglucoisomerase (PGI), phosphoglucomutase (PGM), peroxidase (PRX), and shikimate dehydrogenase (SKD)]. Altogether these 9 loci and 32 clones yielded 28 multi-locus isozymic phenotypes useful for cultivar identification; 24 of the 32 clones were uniquely identified. The allozyme variation in these clones has the average of other long-lived woody perennials of widespread geographic range in temperate regions with insect-pollinated outcrossing breeding systems, secondary asexual reproduction, and animal-dispersed seed. Genetic differentiation among these pawpaw clones, measured by Nei's distance, D, was substantial: 496 pairwise comparisons of genetic distance among the 32 clones indicated that they differed on average of D = 0.068 ± 0.04 and ranged from 0 to 0.188. Cluster analysis (UPGMA) produced a most likely division of the 32 clones into 7 groups; however, these groups did not conform to known pedigree relations. Additional polymorphic enzymes are needed for accurate allozyme-based genetic discrimination.

Genetic similarity among zebra mussel populations within North America and Europe

The zebra mussel Dreissena polymorpha has rapidly established both contiguous and disjunct populations during its spread through eastern North America. If new colonies are founded by small numbers of individuals, populations with markedly different genetic and phenotypic characters could arise (founder effect); this possibility could confound ecological comparisons of populations from different geographic locations. We analyzed genetic differentiation among 18 populations of mussels from the Great Lakes and seven populations from Europe using starch-gel electrophoresis. Analysis of 27 proteins yielded data from 15 polymorphic loci and one monomorphic locus. The data indicated that zebra mussels in North America have the same high genetic variability (Ho = 0.30–0.43) that is found in European populations (Ho = 0.27–0.35) and is typical of molluscs. Little variation appears to have been lost when zebra mussel were transported to North America. Nei's genetic distances between populations were small (0.004–0.028) compared with distances among populations of other mollusc species (0.023–0.184). Like populations from Europe, populations within North America were not highly differentiated, which suggests that founder populations have not been small and (or) frequent genetic mixing has occurred. European populations clustered seperately from North American populations (Nei's distance = 0.058).

An evaluation of genetic distances for use with microsatellite loci.

Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.