Genetic Diversity In Collection Research Articles

Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas.

Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity. We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections. Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual. Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.

Applying the zoo model to conservation of threatened exceptional plant species.

Maintaining a living plant collection is the most common method of ex situ conservation for plant species that cannot be seed banked (i.e., exceptional species). Viability of living collections, and their value for future conservation efforts, can be limited without coordinated efforts to track and manage individuals across institutions. Using a pedigree‐focused approach, the zoological community has established an inter‐institutional infrastructure to support long‐term viability of captive animal populations. We assessed the ability of this coordinated metacollection infrastructure to support the conservation of 4 plant species curated in living collections at multiple botanic gardens around the world. Limitations in current practices include the inability to compile, share, and analyze plant collections data at the individual level, as well as difficulty in tracking original provenance of ex situ material. The coordinated metacollection framework used by zoos can be adopted by the botanical community to improve conservation outcomes by minimizing the loss of genetic diversity in collections. We suggest actions to improve ex situ conservation of exceptional plant species, including developing a central database to aggregate data and track unique individuals of priority threatened species among institutions and adapting a pedigree‐based population management tool that incorporates life‐history aspects unique to plants. If approached collaboratively across regional, national, and global scales, these actions could transform ex situ conservation of threatened plant species.

Genetic diversity in collection of cultivars and varieties of Triticum durum Desf. from Azerbaijan

AFLP analysis of 144 samples of tetraploid wheat species, including cultivars and landraces of Triticum durum from Azerbaijan, was conducted. We obtained 249 fragments, 189 (76%) of which were polymorphic. The Dice genetic similarity index ranged from 0.67 to 0.99. Principal coordinate analysis revealed clear differences between the group of wheat with AuAuBB genome and the group of wheat with AbAbGG genome. Within the group of wheat with AuAuBB genome, differentiation was less pronounced, and this group was not divided into separate subclusters. It was shown that the Azerbaijani varieties of durum wheat were fairly similar to each other and with other species of Triticum durum.

Analysis of molecular genetic diversity in a representative collection of foxtail millet [Setaria italica (L.) P. Beauv.] from different agro-ecological regions of India

Foxtail millet [Setaria italica (L.) P. Beauv.], an important crop of East Asia is known for its drought tolerance and was once an indispensible crop of vast rainfed areas in semi-arid regions in India. In India it is cultivated in Andhra Pradesh, Karnataka, Maharashtra, Tamil Nadu, Rajasthan, Madhya Pradesh, Uttar Pradesh and north eastern states. The grain finds use in several local recipes such as roti (bread), jaula, singal, sirol. Foxtail millet grain contains 12.3% protein, 4.7% fat, 60.6% carbohydrates, and 3.2% ash. The present study was conducted to analyse the genetic diversity among foxtail accessions from different states of India and a few exotic accessions using RAPD and ISSR techniques and identify diverse accessions for use in variety improvement programmes. A set of 125 foxtail millet accessions selected from 11 different agro-ecological regions of India were analyzed using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker techniques. A total of 146 (115 RAPD and 31 ISSR) scoreable markers were generated with 16 RAPD and four ISSR primers. The dendrogram generated using Nei's genetic distances and principal component analyses revealed presence of two clusters and two subclusters in group I. The accessions from Andhra Pradesh, Karnataka, Maharashtra and Uttarakhand were more diverse since they were distributed in both the clusters. There was no clear geographical differentiation observable. The bootstrap support for the major groups identified was strong (above 80%) indicating good statistical support. The average value of Nei and Li's genetic distance was lowest (0.081) for accessions from West Bengal while the collections from Karnataka showed highest dissimilarity (average genetic distance = 0.239). The average genetic distance for all 125 accessions together was 0.177 indicating presence of only moderate genetic diversity in the collections. The analysis of molecular variance indicated that only 2.76% variation was explained by variations among the groups and 11.55% among populations within groups. However the percentage of variation observed within populations was high (85.68). The value of Fst was observed to be very low (0.028) indicating low differentiation of the accessions analysed. The population genetic analysis carried out indicates that highest number of alleles per locus (1.745 ± 0.438) was observed for Andhra Pradesh with 35 accessions. When four eco-geographic regions were considered, the southern region comprising AP, Karnataka and TN showed the highest number of alleles per locus (1.787 ± 0.411). The value of Gst was lowest for south (0.123) and highest for central west (0.455). This indicated that all the landraces from south share common alleles. The gene flow between the accessions from different regions was also observed to be high with the highest migration (3.557) recorded for south.

Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

Pawpaw [Asimina triloba (L.) Dunal.], a tree fruit native to eastern North America, is in the beginning stages of commercialization. Cultivars available in the early 20th century have been lost, and significant genetic erosion may have occurred. Polymorphic microsatellite marker loci were developed from enriched genomic libraries. Five marker loci were used to fingerprint 28 cultivars and 13 selections. For the 41 genotypes, 102 alleles were amplified and major allele frequency (0.16–0.94), number of genotypes (2–27), and allele size (144–343 bp) varied greatly by locus. Four loci were highly polymorphic, as indicated by values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content, but only two alleles were detected at locus Pp-C104. A high level of genetic diversity was observed in the studied genotypes. The Ho (0.68) and He (0.70) were similar and indicated few null alleles. In the 41 genotypes, 39 unique fingerprints were observed. These new microsatellite marker loci will be useful for cultivar fingerprinting, management of collections, and investigation of genetic diversity in collections and wild populations. Grouping of genotypes in an unweighted pair group method with arithmetic mean dendrogram was generally consistent with their origins.

Fine scale genetic structure in a wild soybean (Glycine soja) population and the implications for conservation.

• The fine-scale spatial distribution of a wild soybean (Glycine soja Sieb. et Zucc) population was measured using kinship coefficients and spatial autocorrelation coefficients to reveal fine-scale spatial patterns of genetic structure for guiding collection in ex situ conservation. • Individual families (100) of a single population were sampled in Jiangwan (Shanghai, China) and their specific locations mapped. Individual plants were genotyped for 331 ISSR loci from 15 selective ISSR primers; 45% were demonstrated to be polymorphic. • Pairwise kinship coefficients between individuals were calculated, and then regressed based on the spatial distance between individuals. The results indicated a close genetic relationship among individual families in the patch with a diameter of c. 30m. Spatial autocorrelation analysis suggested that there were significant clusters of genes within the population; c. 81.4% of the loci were found to be positively correlated in the first two distance classes (0-10m). • The results suggest, for conservation genetics, sampling within a wild soybean population should be conducted at 10 m intervals across the entire population to optimize the genetic diversity in collections taken from that population.

Spatial genetic structure in populations of Cymbidiumgoeringii(Orchidaceae).

The fine-scale population genetic structure of Cymbidium goeringii (Orchidaceae), a small herbaceous perennial, was analyzed using spatial autocorrelation statistics. All visible individuals (138 and 110, respectively) within 20 × 40 m areas of each of two populations were sampled and their locations were mapped. Individual plants were genotyped for 14 allozyme loci, and Moran's spatial autocorrelation statistics were calculated for a large numbers of alleles. Values of Moran's I-statistics were statistically significant in 35 (19.4%) to 36 (16.4%) of 180 and 220 cases respectively for the two populations, and the overall correlograms were significant for 11 (61.1%) to six (27.3%) of 18 and 22 alleles, respectively. The results also indicate that genetic similarity was shared among individuals within up to a scale of 14 m distance, and this is partly due to a combination of limited pollen dispersal and long distance seed dispersal by wind. One important implication is that, from the viewpoint of conservation genetics, sampling within populations should be conducted at 14-16 m intervals in order to optimize the genetic diversity in collections from population.