scholarly journals Genetic Structure of a Loblolly Pine Breeding Population at Brazil

ISRN Forestry ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Juliane Rezende Mercer ◽  
Milena de Luna Alves Lima ◽  
Antonio Rioyei Higa ◽  
Chirlei Glienke ◽  
Marina Isabel Mateus de Almeida
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Loblolly Pine ◽  
A Priori ◽  
Breeding Population ◽  
Zone Model ◽  
Wood Volume ◽  
Second Best ◽  
Seed Sources ◽  
Maternal Generation

The genetic structure of a Brazilian loblolly pine (Pinus taeda L.) breeding population, represented by 120 open-pollinated families, was determined using Bayesian inference and genotypes of 15 microsatellite (simple sequence repeat (SSR)) loci in 1,130 seedling progeny. The 120 maternal parents had been phenotypically selected about 15 years ago for wood volume in five different forestry plantations (FPs) in the south of Brazil. Additional selection for wood volume, based on a previous progeny test, was applied to the first best (i) and second best (ii) tree per block within each family. We adopted a procedure of “learning samples” to find the most likely number of inferred genetic clusters (K) or ancestral populations. The first hypothesis that was rejected was that the most probable value of K=5 was coincident with the five FPs, since the FPs were, a priori, assumed to be from 5 different backgrounds or origins. It was used the familiar structure of the population to infer the genotypes of maternal ancestors. It was concluded that the maternal generation is the most likely to have been planted by the mixture of three different seed sources or origins, that there are five genetic groups (K=5) in the population of progeny, and that they have been formed from the occurrence of assortative mating and also from a strong pressure in the selection within families. The trees with the best genetic value (i) maintained a higher genetic variability when compared to the trees of second best performance (ii), with higher values of heterozygosity and of numbers of maternal alleles that were kept the same. The migration model that best explains the results is the contact zone model. The population differentiation (FST) was 2-3 times higher in offspring than in relation to the maternal generation. The relevancy of the results and the way they were explored may be of value both for studies of population genetics, as for plant breeding programs, since they help monitoring the population's genetic variability during generations of selection.

scholarly journals PERIODIC SELECTION, INFECTIOUS GENE EXCHANGE AND THE GENETIC STRUCTURE OF E. COLI POPULATIONS

Genetics ◽  
1981 ◽  
Vol 99 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Bruce R Levin
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Bacterial Species ◽  
A Priori ◽  
Natural Populations ◽  
Gene Exchange ◽  
Effective Population ◽  
Bacterial Populations ◽  
E Coli ◽  
Population Sizes

ABSTRACT As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.—With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.—Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations of the interpretation of protein variation and the neutral gene hypothesis are discussed.

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

Clonal and nonclonal genetic structure of subarctic black spruce (Picea mariana) populations in Yukon territory

Botany ◽  
2011 ◽  
Vol 89 (2) ◽  
pp. 133-140 ◽  
Author(s):  
Marios Viktora ◽  
Rodney A. Savidge ◽  
Om P. Rajora
Keyword(s):  
Genetic Structure ◽  
Picea Mariana ◽  
Black Spruce ◽  
A Priori ◽  
Nuclear Genome ◽  
Yukon Territory ◽  
Fire Disturbance ◽  
Clone Size ◽  
Flat Terrain ◽  
Individual Trees

Black spruce (Picea mariana) reproduces sexually from seeds and asexually by layering. There is a prevalent concept that clonal reproduction maintains populations of this species in the subarctic and arctic regions. We used microsatellite DNA markers of the nuclear genome to investigate the genetic structure of montane and subalpine black spruce populations from the Western Yukon Plateau in relation to this concept. Sixty individual trees at a minimum distance of 4 m from each other were sampled from each of four populations and individual trees were genotyped for eight microsatellite loci. Each of the 60 individuals from three montane pure black spruce populations growing on flat terrain at relatively low elevations had unique multilocus genotypes, indicating an absence of clonal structure in those populations. However, in an anthropologically undisturbed climax white spruce-dominated subalpine black spruce population on a northwest slope near Mount Nansen, the majority of the sampled individuals belonged to eight genetically distinct clones (genets). Clone size differed by altitude, the dominant genet being nearest the timberline–tundra ecotone. The results indicate that black spruce reproduction is variable and adaptive, being primarily sexual in flat-terrain montane populations previously subjected to fire disturbance, but mixed vegetative–sexual in the anthropogenically undisturbed subalpine population. This study is the first to employ molecular markers a priori to examine the mode of reproduction in natural black spruce populations.

scholarly journals Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus

2018 ◽  
Vol 124 (4) ◽  
pp. 521-529 ◽  
Author(s):  
Gancho T Slavov ◽  
Christopher L Davey ◽  
Maurice Bosch ◽  
Paul R H Robson ◽  
Iain S Donnison ◽  
...  
Keyword(s):  
Biomass Yield ◽  
A Priori ◽  
Biomass Productivity ◽  
Breeding Population ◽  
Index Selection ◽  
Correlated Responses ◽  
Morphometric Traits ◽  
Need To Evaluate ◽  
Breeding Programmes ◽  
Selection Intensities

Abstract Background Miscanthus has potential as a biomass crop but the development of varieties that are consistently superior to the natural hybrid M. × giganteus has been challenging, presumably because of strong G × E interactions and poor knowledge of the complex genetic architectures of traits underlying biomass productivity and climatic adaptation. While linkage and association mapping studies are starting to generate long lists of candidate regions and even individual genes, it seems unlikely that this information can be translated into effective marker-assisted selection for the needs of breeding programmes. Genomic selection has emerged as a viable alternative, and prediction accuracies are moderate across a range of phenological and morphometric traits in Miscanthus, though relatively low for biomass yield per se. Methods We have previously proposed a combination of index selection and genomic prediction as a way of overcoming the limitations imposed by the inherent complexity of biomass yield. Here we extend this approach and illustrate its potential to achieve multiple breeding targets simultaneously, in the absence of a priori knowledge about their relative economic importance, while also monitoring correlated selection responses for non-target traits. We evaluate two hypothetical scenarios of increasing biomass yield by 20 % within a single round of selection. In the first scenario, this is achieved in combination with delaying flowering by 44 d (roughly 20 %), whereas, in the second, increased yield is targeted jointly with reduced lignin (–5 %) and increased cellulose (+5 %) content, relative to current average levels in the breeding population. Key Results In both scenarios, the objectives were achieved efficiently (selection intensities corresponding to keeping the best 20 and 4 % of genotypes, respectively). However, the outcomes were strikingly different in terms of correlated responses, and the relative economic values (i.e. value per unit of change in each trait compared with that for biomass yield) of secondary traits included in selection indices varied considerably. Conclusions Although these calculations rely on multiple assumptions, they highlight the need to evaluate breeding objectives and explicitly consider correlated responses in silico, prior to committing extensive resources. The proposed approach is broadly applicable for this purpose and can readily incorporate high-throughput phenotyping data as part of integrated breeding platforms.

scholarly journals Genetic variability in physic nuts cultivated in Northeastern Brazil

2013 ◽  
Vol 43 (6) ◽  
pp. 978-984 ◽  
Author(s):  
Vanice Dias Oliveira ◽  
Allivia Rouse Carregosa Rabbani ◽  
Ana Veruska Cruz da Silva ◽  
Ana da Silva Lédo
Keyword(s):  
Molecular Markers ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Northeastern Brazil ◽  
Jaccard Coefficient ◽  
Physic Nut ◽  
Genetic Structure And Diversity

This research had as objective to characterize genetically individuals of physic nut cultivated in experimental areas in Sergipe, Brazil by means of RAPD molecular markers. Leaves of 40 individuals were collected and DNA was isolated using CTAB 2% method. Were used 30 primers RAPD for DNA amplification, and this data was used to estimate the genetic similarity among the pairs of individuals, using Jaccard coefficient, and group them out for the UPGMA method. Also, the genetic structure and diversity of the populations were assessed using AMOVA. Of the 100 fragments generated, 29 of were polymorphic. A similarity average of 0.54 among the individuals was found and the amplitude similarities varied from 0.18 to 1.00. One of them (U5) was unit clusters and formed by the most divergent individuals. AMOVA indicated that there is more variation within (63%) the population. In conclusion, it was possible verify genetic variability in physic nut using RAPD markers at these experimental areas.

Nutrient Content of the Aboveground Tissue of 12-week-old Loblolly Pine Intraprovenance and Interprovenance Crosses

1975 ◽  
Vol 5 (4) ◽  
pp. 592-598 ◽  
Author(s):  
R. A. Woessner ◽  
C. B. Davey ◽  
B. E. Crabtree ◽  
J. D. Gregory
Keyword(s):  
Loblolly Pine ◽  
Dry Matter ◽  
Dry Weight ◽  
Nutrient Content ◽  
Seed Source ◽  
Good Linear ◽  
Available Nutrients ◽  
Seed Sources ◽  
Linear Relationships ◽  
Aboveground Tissue

Nutrient content (P, K, Ca, Mg) of the aboveground tissue of a series of full-sib loblolly crosses was found to vary by genotype. Variability among and within seed sources is indicated for the ability to absorb Ca and Mg. Absorption of P and K was not found to be dependent on seed source, but the full-sib crosses differ. Good linear relationships were found between plant dry weight and weight of element but not between plant dry weight and percentage of element. Certain highly efficient crosses can be expected to be good producers of dry matter on sites low in available nutrients.

scholarly journals Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 681 ◽  
Author(s):  
Huiquan Zheng ◽  
Dehuo Hu ◽  
Ruping Wei ◽  
Shu Yan ◽  
Runhui Wang
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Breeding Population ◽  
Population Diversity ◽  
Chinese Fir ◽  
High Density ◽  
Population Structure Analysis ◽  
Snp Panel

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

The effect of genotype on biomass and nutrient content in 11-year-old loblolly pine plantations

1979 ◽  
Vol 9 (2) ◽  
pp. 224-230 ◽  
Author(s):  
P. E. Pope
Keyword(s):  
Loblolly Pine ◽  
Plant Biomass ◽  
Soil Nutrient ◽  
Dry Weight ◽  
Nutrient Content ◽  
Seed Source ◽  
Elemental Content ◽  
Total N ◽  
Seed Sources ◽  
Hilly Region

Dry weights and nutrient contents of all aboveground biomass components were estimated for four seed sources of 11-year-old loblolly pine (Pinustaeda L.) grown in plantations of the same spacing on an old-field site of high quality in the hilly region of north-central Arkansas, U.S.A. Soil nutrient content was estimated to a depth of 0.61 m. Stand data averaged over all seeds sources are in agreement with published reports for dry weight and nutrient accumulation for loblolly pine if differences associated with seasonal variation are considered. Seed source significantly affected total dry matter and nutrient accumulations. Estimated total aboveground mean annual accumulation of biomass for the four seed sources ranged from 5.99 × 103 to 11.17 × 103 kg/ha per year. Elemental accumulation (kilograms per hectare per year) ranged from 14.06 to 23.66 for N, 1.54 to 3.45 for P, and 6.96 to 18.43 for K. On the average, trees comprise 84% of the aboveground plant biomass and contain 76% of the N, 77% of the P, and 90%, of the K associated with plant tissue. The significant influence of seed source on these stand values can affect the potential impact of short rotation, total tree harvesting on long-term site productivity. The elemental content of the tree biomass ranged from 7 to 11% of the total N, 20 to 35% of the P, and 14 to 30% of the K in the soil–litter–plant system.

Sign in / Sign up

Export Citation Format

Share Document