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The use of biotechnology in the conservation of tropical germplasm.

The rapid erosion of the genetic diversity of both wild and cultivated plants has recently attracted more and more international concern. As a consequence, germplasm conservation techniques have become accessible to protect the third world's germplasm diversity. Several approaches are used for germplasm conservation and utilization. The evaluation and use of these techniques has to be focussed with one important objective; to preserve with as much integrity as possible, the genetic variability of the selected species. Questions have risen about the best way to preserve genetic diversity of the humid tropics, since it is being recognized that these conditions hold much of the world's gene pool of plants. Seed banks are considered the best system for orthodox seed storage. For many tropical species that cannot support dehydration, tissue culture and cryoconservation are the best alternative. Important considerations regarding the adaptation of modern techniques to tropical species have to be carefully analyzed. Quantitative studies of genetic indices of somaclonal variation, or types or mutant plants can be observed. Consideration of plant germplasm as a base for genetic improvement has come a long way, but much remains to be done, particularly, with the plant diversity that exists in the tropics. All efforts to conserve and use genetic resources will contribute to the benefit of future human generations.

Journal Article↗

Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Published data on allele frequencies at isozyme loci in inbreeding and outbreeding plant species were analyzed to examine intraspecific variation in gene diversity and effective population size (Ne). Compared with outbreeders, inbreeding species showed markedly greater variation among populations in average values of Nei's gene diversity statistic. Effective population size was estimated by assuming that the variation observed at isozyme loci is selectively neutral. Inbreeding species showed greater levels of variation in Ne than did outbreeders, although the upper range of Ne was similar in the two classes of species. The results suggest that there may be considerable genetic variation and potential for evolutionary change in some but not all populations of inbreeders. Moreover, these findings are important with respect to the conservation of genetic resources. In particular, that the amount of intraspecific variation in population genetic diversity and Ne differs between inbreeding and outbreeding species should be taken into account in sampling efforts designed to optimize the diversity of germplasm collections.

Journal Article↗

Cryopreservation of gametes and embryos of non-domestic species.

Many species of mammals are threatened or endangered. Methods of assisted reproduction that are being used with increasing frequency to produce offspring of domestic animals and humans are often viewed as offering innovative ways to reproduce non-domestic species as well. Uncounted millions of live young of domestic or laboratory species have been produced from gametes and embryos stored at -70 degrees C or below, sometimes for as long as 25 to 35 yrs. Such methods of cryopreservation are now being applied with increasing frequency and urgency to preserve gametes and embryos of non-domestic and threatened species to establish "genome resource banks" or "frozen zoos." But levels of success to produce live young from such cryopreserved gametes or embryos vary considerably from species to species, as well as from individual to individual. It is sometimes thought that differences among species in fundamental characteristics of their gametes may determine the efficacy of cryopreservation and the production of live young. However, it may not be that ineffective cryopreservation is responsible for low success rates. Rather, the limiting factor may be insufficient information and knowledge of the most basic reproductive biology of such non-domestic species. Even standard methods of cryopreservation may be completely adequate to act as a "temporary" expedient to preserve germplasm of non-domestic species to permit time to acquire a fuller understanding of the biology and behavior of non-domestic species.

Animals↗

Animal genetic resources in Brazil: result of five centuries of natural selection.

Brazil has various species of domestic animals, which developed from breeds brought by the Portuguese settlers soon after their discovery. For five centuries, these breeds have been subjected to natural selection in specific environments. Today, they present characteristics adapted to the specific Brazilian environmental conditions. These breeds developed in Brazil are known as "Crioulo," "local," or naturalized. From the beginning of the 20th century, some exotic breeds, selected in temperate regions, have begun to be imported. Although more productive, these breeds do not have adaptive traits, such as resistance to disease and parasites found in breeds considered to be "native." Even so, little by little, they replaced the native breeds, to such an extent that the latter are in danger of extinction. In 1983, to avoid the loss of this important genetic material, the National Research Center for Genetic Resources and Biotechnology (Cenargen) of the Brazilian Agricultural Research Corporation (Embrapa) decided to include conservation of animal genetic resources in its research program Conservation and Utilization of Genetic Resources. Until this time, they were only concerned with conservation of native plants. Conservation has been carried out by various research centers of Embrapa, universities, state research corporations, and private farmers, with a single coordinator at the national level, Cenargen. Specifically, conservation is being carried out by conservation nuclei, which are specific herds in which the animals are being conserved, situated in the habitats where the animals have been subjected to natural selection. This involves storage of semen and embryos from cattle, horses, buffaloes, donkeys, goats, sheep, and pigs. The Brazilian Animal Germplasm Bank is kept at Cenargen, which is responsible for the storage of semen and embryos of various breeds of domestic animals threatened with extinction, where almost 45,000 doses of semen and more than 200 embryos exist presently. An important challenge for this program is to make the different segments of society realize the importance of the conservation of animal genetic resources.

Adaptation, Physiological↗

CMD: a Cotton Microsatellite Database resource for Gossypium genomics.

BACKGROUND: The Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. CONCLUSION: The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

Chromosome Mapping↗

Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia.

Amid escalating water scarcity and groundwater depletion, halophytes such as Salicornia (Amaranthaceae) represent valuable models for extreme salt tolerance and hold promise for saltwater-based agriculture. Here, we show chromosome-scale genome assemblies for six Salicornia species, revealing four distinct subgenomes, reconciling our assemblies with two existing reference genomes (S. ramosissima UK and S. europaea China), correcting chromosome numbering and orientation. Comparative analyses across ploidy levels demonstrate genome expansion in North American lineages driven by Gypsy retrotransposons, and lineage-specific expansions of two gene families implicated in stress metabolism. Phylogenetic and population-structure analyses of a global resequencing panel of 318 accessions resolve interspecific relationships and establish curated germplasm collections for future crop breeding. Genetic analyses uncover a contrasting population-genetic signal on chromosome 6A between two species, highlighting an OSCA calcium-permeable channel gene as a candidate locus for osmotic adaptation. Together, these resources establish a genomic framework for Salicornia that supports evolutionary studies of halophyte adaptation and crop development.

Chenopodiaceae↗

Application of TILLING in plant improvement.

TILLING (Targeting induced local lesions in genomes) is a general reverse-genetic strategy that is used to locate an allelic series of induced point mutations in genes of interest. High-throughput TILLING allows the rapid and cost-effective detection of induced point mutations in populations of chemically mutagenized individuals. The technique can be applied not only to model organisms but also to economically important organisms in plants. Owing to its full of advantages such as simple procedure, high sensitivity, and high efficiency, TILLING provides a powerful approach for gene discovery, DNA polymorphism assessment, and plant improvement. Coupled with other genomic resources, TILLING and EcoTILLING can be used immediately as a haplotyping tool in plant breeding for identifying allelic variation in genes exhibiting expression correlating with phenotypes and establishing an allelic series at genetic loci for the traits of interest in germplasm or induced mutants.

Alleles↗

Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.).

Molecular genetic marker development in perennial ryegrass has largely been dependent on anonymous sequence variation. The availability of a large-scale EST resource permits the development of functionally-associated genetic markers based on SNP variation in candidate genes. Genic SNP loci and associated haplotypes are suitable for implementation in molecular breeding of outbreeding forage species. Strategies for in vitro SNP discovery through amplicon cloning and sequencing have been designed and implemented. Putative SNPs were identified within and between the parents of the F(1)(NA(6) x AU(6)) genetic mapping family and were validated among progeny individuals. Proof-of-concept for the process was obtained using the drought tolerance-associated LpASRa2 gene. SNP haplotype structures were determined and correlated with predicted amino acid changes. Gene-length LD was evaluated across diverse germplasm collections. A survey of SNP variation across 100 candidate genes revealed a high frequency of SNP incidence (c. 1 per 54 bp), with similar proportions in exons and introns. A proportion (c. 50%) of the validated genic SNPs were assigned to the F(1)(NA(6) x AU(6)) genetic map, showing high levels of coincidence with previously mapped RFLP loci. The perennial ryegrass SNP resource will enable genetic map integration, detailed LD studies and selection of superior allele content during varietal development.

Breeding↗

Genetic diversity in and conservation strategy considerations for Navajo Churro sheep.

The objectives of this study were to 1) evaluate the genetic diversity of Navajo-Churro sheep using pedigree information; 2) examine the distribution of the Navajo-Churro population; and 3) evaluate the effect of breeder dynamics on genetic conservation of the breed. Pedigree data and breeder information (city and state) were obtained from the Navajo-Churro Sheep Breed Association. Inbreeding coefficients were calculated for each individual animal using pedigree information. A geographic information system program was used to divide the United States into four regions and overlay breeder locations, flock size, and flock inbreeding level. The small correlation between level of inbreeding and flock size (r = -0.07, P = 0.07) indicated that inbreeding levels are not different across flock sizes. The mean flock inbreeding levels ranged from 0 to 11% across regions. The level of inbreeding did not differ among regions (P = 0.15), except for Region 4 (Kansas and Missouri; P = 0.001). The number of breeders registering sheep averaged 34 per year. Most of the breeders were transient, with only eight breeders maintaining ownership for more than 7 yr. Average inbreeding level for 2000 was found to be 1.2%, with a linear increase in inbreeding of 0.1%/yr over the period studied, suggesting a minimal loss of genetic diversity for the Navajo-Churro. However, given the relatively small effective population size (92) and the transient nature of the breeders, development of an ex situ cryo-preserved germplasm bank may be the best long-term strategy for maintaining this breed's genetic diversity.

Animals↗

A changing climate for grassland research.

Here, we review the current genetic approaches for grass improvement and their potential for the enhanced breeding of new varieties appropriate for a sustainable agriculture in a changing global climate. These generally out-breeding, perennial, self-incompatible species present unique challenges and opportunities for genetic analysis. We emphasise their distinctiveness from model species and from the in-breeding, annual cereals. We describe the modern genetic approaches appropriate for their analysis, including association mapping. Sustainability traits discussed here include stress resistance (drought, cold and pathogeneses) and favourable agronomic characters (nutrient use efficiency, carbohydrate content, fatty acid content, winter survival, flowering time and biomass yield). Global warming will predictably affect temperature-sensitive traits such as vernalisation, and these traits are under investigation. Grass biomass utilisation for carbon-neutral energy generation may contribute to reduced atmospheric carbon emissions. Because the wider potential outcomes of climate change are unpredictable, breeders must be reactive to events and have a range of well-characterised germplasm available for new applications.

Agriculture↗

Advancements in cryopreservation of domestic animal embryos.

The development of embryo freezing technologies revolutionized cattle breeding. Since then, advancements in cryobiology, cell biology, and domestic animal embryology have enabled the development of embryo preservation methodologies for our other domestic animal species, including sheep and goats. Recently, technologies have been developed to cryopreserve pig embryos, notorious for their extreme sensitivity to cooling; horse embryo cryopreservation is in its infancy. While cryopreservation can enhance the utilization of in vitro embryo production technologies, cryosurvival of in vitro-produced (IVP) or micromanipulated embryos is less than that of in vivo-derived embryos. This review outlines recent efforts in livestock embryo cryopreservation. In the near future, use of preserved embryos could be a routine breeding alternative for all livestock producers providing 1) preservation methods for maternal germplasm, 2) global genetic transport, 3) increased selection pressure within herds, 4) breeding line regeneration or proliferation, and 5) methodology for genetic rescue.

Animals↗

Agrobiodiversity with emphasis on plant genetic resources.

The science of agrobiodiversity has emerged during the last 10 years. We review here the most important aspects of biodiversity for conservation. One of the aims of agrobiodiversity research is to introduce or to re-introduce into present-day agriculture and horticulture more diversity from gene banks, botanical or zoological gardens, and other secondary sources of diversity. To enlarge the basis of agricultural and horticultural resources for human and animal nutrition, a sustainable use of these native and cultivated resources is necessary, including animal and plant genetic resources. The total number of botanical plant species cultivated as agricultural or horticultural crops is estimated at almost 7,000. However, only 30 major crop species "feed the world". Comparable numbers of animal species have been lost. The reduction in crop species and variety diversity, in particular, has led to the establishment of germplasm collections, so called gene banks, or ex situ collections. Six million plant accessions are conserved in gene banks worldwide. All these accessions belong to a very limited number of species. About half of them are advanced cultivars or breeders' lines, and only a third are landraces or old cultivars. Approximately 15% are wild relatives of crop species and weeds. Among other obvious gaps, minor crops and underutilized species are underrepresented in these collections, particularly primitive cultivars and wild relatives from the centers of origin, diversity, and cultivation. To date, only a third of all gene bank accessions have been fully characterized.

Agriculture↗

Development of national animal genetic resource programs.

Globally, animal genetic resources are contracting due to economic forces. As a result, during the 1990s there was a dramatic increase in national animal genetic resource activities. Many national programmes were initiated and the Food and Agriculture Organisation of the United Nations played a prominent role in coalescing national actions. Nationally, programmes have been initiated that comprise of in situ, ex situ and information-exchange efforts. A critical element to national conservation efforts is the development of cryopreserved collections of germplasm. Several countries have initiated substantial multispecies collections of cryopreserved germplasm. The selection of animals within breeds of interest is an important consideration in building cryopreserved collections. Animal selection should be based on a lack of genetic relationship, with sufficient numbers of animals to ensure the capture of rare alleles. Major issues facing repository development and genetic conservation are: (1) that all breeds are in need of genetic diversity management; (2) a better understanding of in situ breed population dynamics is needed; and (3) the concept that repository collections can be used by a broad range of clientele across time as well as during emergency situations.

Animals↗

Role of bougainvilleas in mitigation of environmental pollution.

Environmental pollution adversely affects health of the people. Industrialization, urbanization, over exploitation of natural resources and increasing number of automobiles have aggravated the pollution manifold though there are various ways to mitigate the environmental pollution. Bio-remediation by using selected plant species is an effective method to control pollution which is universally accepted. Bougainvillea is a pollution tolerant plant and can help in the mitigation of air pollution besides its ornamental value in the landscaping. From the rich germplasm collection in NBRI Botanical Garden, tolerant plants have been experimented for road side plantation in view of mitigating the environmental pollution.

Air Pollutants↗

Cryopreservation of pig embryos.

The changing global needs for food and animal products require the development of breeding strategies for maximizing genetic improvement while maintaining genetic diversity. Genetic diversity can be conserved by using separate breeding herds; however, they may be expensive to maintain and inbreeding becomes a major concern. Alternative methods are needed to preserve valuable genetic resources in a reasonable and economic manner. Embryo cryopreservation allows indefinite storage in vitro at subambient temperatures where metabolism and other cellular functions are greatly reduced or cease, and upon recovery from storage, normal developmental competence can be resumed. Storage and transportation require little maintenance and there is no expense in animal care and little concern about disease transmission. Although there are methods for routine cryopreservation of germplasm and embryos of most livestock species, development of this technology in the pig industry is far behind and has abated improvements in genetic potential. Pig embryos are very sensitive to hypothermic conditions, and this limits their ability to withstand many conventional methods of preservation. Much research has focused on the high lipid content of pig embryos, and its role in hypothermic sensitivity and cryosurvival. Many studies have reported the conventional freezing of pig embryos, and vitrification has shown promise of eluding the difficulties associated with cooling sensitivity and ice crystallization. Recent research suggests that the embryonic cytoskeleton is susceptible to damage during cryopreservation, and this cellular disruption may be averted by using cytoskeletal stabilizers before preservation. Embryos cryopreserved by conventional freezing and vitrification under the influence of cytoskeletal stabilization have resulted in pregnancies or live offspring from recipient females after surgical transfer. Although cryopreservation technology is less advanced in pigs than in other livestock species, promising research shows evidence that researchers are close to achieving a methodology for preserving pig embryos.

Animals↗

Random amplified polymorphic DNA analysis of Indian scented basmati rice (Oryza sativa L.) germplasm for identification of variability and duplicate accessions, if any.

Genetic variation among the seventeen basmati rice accessions collected from the farmers' fields located at different places in India was analyzed using ten arbitrary tenmer oligonucleotide primers by the random amplified polymorphic DNA (RAPD) method. The number of polymorphic/monomorphic bands among the pairwise combinations of the accessions and the total number of bands were determined to categorize all the accessions in different groups of similarity and dissimilarity at the genetic level. The procedure described also allows the identification and discrimination of the individual genotypes of basmati rice including the identification of the duplicates in genetic resource collections.

DNA, Plant↗

[Genetic diversity of gliadin in wild germplasm of Elymus nutans Griseb].

Acid polyacrylamide gel electrophoresis (A-PAGE) was used to detect the gliadin genetic polymorphism among thirty-three wild accessions of Elymus nutans Griseb collected from four provinces and regions in China (Xinjiang, Qinghai, Sichuan and Tibet). The follows results were obtained. (1) A total of 38 bands were detected in all accessions, 92.1% were polymorphic bands. The average number of Shannon index to four electrophoretic zones was 0.55. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.36 to 0.94, and the average Nei's coefficient was 0.63. These results suggested that there was rich genetic polymorphism among the tested wild resources of Elymus nutans Griseb. (2) 33 wild accessions can be clustered into seven groups at GS = 0.67 level on dendrogram. The principal coordinates (PCA) reflected almost the same relationships among the studied materials as shown in cluster analysis. Moreover, the groups from the same origin frequently clustered into one group. The findings implied that a correlation among gliadin patterns, geographical and ecological environment. (3) Genetic differentiation between and within five eco-geographical groups of Elymus nutans was estimated by Shannon's diversity index, which shown that 42.94% genetic variance existed within group, and 50.76% genetic variance was among groups. This result might be correlative to mainly self-pollinated breeding system of E. nutans. (4) UPGMA cluster analysis based on Nei's unbiased measures of genetic identity was assayed for five geographical groups of Elymus nutans, indicating that there was a significantly positive correlation between genetic differentiation and geographical habits among the five groups.

China↗

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

BACKGROUND AND AIMS: Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS: Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS: Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS: These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

Cacao↗