scholarly journals Use of genetic markers to build a new generation of Eucalyptus pilularis breeding population

2015 ◽  
Vol 64 (1-6) ◽  
pp. 170-181 ◽  
Author(s):  
Paulo H. M. Da Silva ◽  
M. Shepherd ◽  
D. Grattapaglia ◽  
A. M. Sebbenn
Keyword(s):  
Genetic Diversity ◽  
Recurrent Selection ◽  
Breeding Population ◽  
Generation Times ◽  
Plantation Species ◽  
Lower Fertility ◽  
Eucalyptus Pilularis ◽  
Early Performance ◽  
New Generation ◽  
Modern Breeding

Abstract Tree improvement generally proceeds by incremental gains obtained from recurrent selection in large diverse populations but is slow due to long generation times and delay till trees reach assessment age. This places a premium upon extracting data from historic introductions used to found landraces when reinstating modern breeding programs. The value of such resources, however, may be degraded due to a lack of records on germplasm origins, pedigrees and early performance, but DNA technology may help recoup some of this value. Eucalyptus pilularis (subgenus Eucalyptus) is regarded as a premier hardwood plantation species for saw log and poles in Australia, but has not been used extensively despite early introductions and testing in many countries overseas. Here we use DNA fingerprinting to assess genetic diversity and inbreeding in historic introductions of E. pilularis to evaluate this resource in advance of a reinvigorated breeding effort for this species in Brazil. As expected, based on the available documentation for the introductions, genetic diversity relative to Australian reference populations does not appear to be compromised, and there was unlikely to be excessive inbreeding. Also, favorable, was the likelihood that further selections should not unduly increase the relationship in the next generation. Interestingly, we note the importance of testing widely adapted sources of germplasm when making introductions, as provenances which performed poorly in tests on productive sites in Australia, may have value when matched with lower fertility sites overseas.

Multivariate analysis to quantify genetic diversity and family selection in sour passion fruit under recurrent selection

Euphytica ◽  
2021 ◽  
Vol 217 (1) ◽  
Author(s):  
Amanda Fernanda Nunes Ferreira ◽  
Willian Krause ◽  
Maria Helena Menezes Cordeiro ◽  
Alexandre Pio Viana ◽  
Eileen Azevedo Santos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Recurrent Selection ◽  
Passion Fruit ◽  
Family Selection ◽  
Sour Passion Fruit

scholarly journals Loss of Genetic Diversity with Captive Breeding and Re-Introduction: A Case Study on Pateke/Brown Teal (Anas chlorotis)

2021 ◽  
Author(s):  
◽  
Gemma Bowker-Wright
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Captive Breeding ◽  
Barrier Island ◽  
Breeding Population ◽  
Island Population ◽  
Wildlife Sanctuary ◽  
Management Options ◽  
Introduced Populations ◽  
Loss Of Genetic Diversity

<p>Pateke/brown teal (Anas chlorotis) have experienced a severe population crash leaving only two remnant wild populations (at Great Barrier Island and Mimiwhangata, Northland). Recovery attempts over the last 35 years have focused on an intensive captive breeding programme which breeds pateke, sourced almost exclusively from Great Barrier Island, for release to establish re-introduced populations in areas occupied in the past. While this important conservation measure may have increased pateke numbers, it was unclear how much of their genetic diversity was being retained. The goal of this study was to determine current levels of genetic variation in the remnant, captive and re-introduced pateke populations using two types of molecular marker, mitochondrial DNA (mtDNA) and microsatellite DNA. Feathers were collected from pateke at Great Barrier Island, Mimiwhangata, the captive breeding population and four re-introduced populations (at Moehau, Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island). DNA was extracted from the base of the feathers, the mitochondrial DNA control region was sequenced, and DNA microsatellite markers were used to genotype individuals. The Great Barrier Island population was found to have only two haplotypes, one in very high abundance which may indicate that historically this population was very small. The captive breeding population and all four re-introduced populations were found to contain only the abundant Great Barrier Island haplotype as the vast majority of captive founders were sourced from this location. In contrast, the Mimiwhangata population contained genetic diversity and 11 haplotypes were found, including the Great Barrier Island haplotype which may have been introduced by captive-bred releases which occurred until the early 1990s. From the microsatellite results, a loss of genetic diversity (measured as average alleles per locus, heterozygosity and allelic richness) was found from Great Barrier Island to captivity and from captivity to re-introduction. Overall genetic diversity within the re-introduced populations (particularly the smaller re-introduced populations at Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island) was much reduced compared with the remnant populations, most probably as a result of small release numbers and small population size. Such loss of genetic diversity could render the re-introduced populations more susceptible to inbreeding depression in the future. Suggested future genetic management options are included which aim for a broader representation of genetic diversity in the pateke captive breeding and release programme.</p>

scholarly journals Retraction Note: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Karim Sorkheh ◽  
Mehrana Koohi Dehkordi ◽  
Sezai Ercisli ◽  
Attila Hegedus ◽  
Júlia Halász
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Dna Markers ◽  
High Genetic Diversity ◽  
Link Type ◽  
New Generation ◽  
Wild Almond

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72522-x

scholarly journals Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs

2021 ◽  
Author(s):  
Peter Civan ◽  
Renaud Rincent ◽  
Alice Danguy-Des-Deserts ◽  
Jean-Michel Elsen ◽  
Sophie Bouchet
Keyword(s):  
Genetic Diversity ◽  
Quantitative Genetics ◽  
Genetic Gain ◽  
Recurrent Selection ◽  
Prediction Models ◽  
Population Genomics ◽  
Breeding Program ◽  
Breeding Programs ◽  
Sequencing Technologies ◽  
Genetic Value

AbstractThe breeding efforts of the twentieth century contributed to large increases in yield but selection may have increased vulnerability to environmental perturbations. In that context, there is a growing demand for methodology to re-introduce useful variation into cultivated germplasm. Such efforts can focus on the introduction of specific traits monitored through diagnostic molecular markers identified by QTL/association mapping or selection signature screening. A combined approach is to increase the global diversity of a crop without targeting any particular trait.A considerable portion of the genetic diversity is conserved in genebanks. However, benefits of genetic resources (GRs) in terms of favorable alleles have to be weighed against unfavorable traits being introduced along. In order to facilitate utilization of GR, core collections are being identified and progressively characterized at the phenotypic and genomic levels. High-throughput genotyping and sequencing technologies allow to build prediction models that can estimate the genetic value of an entire genotyped collection. In a pre-breeding program, predictions can accelerate recurrent selection using rapid cycles in greenhouses by skipping some phenotyping steps. In a breeding program, reduced phenotyping characterization allows to increase the number of tested parents and crosses (and global genetic variance) for a fixed budget. Finally, the whole cross design can be optimized using progeny variance predictions to maximize short-term genetic gain or long-term genetic gain by constraining a minimum level of diversity in the germplasm. There is also a potential to further increase the accuracy of genomic predictions by taking into account genotype by environment interactions, integrating additional layers of omics and environmental information.Here, we aim to review some relevant concepts in population genomics together with recent advances in quantitative genetics in order to discuss how the combination of both disciplines can facilitate the use of genetic diversity in plant (pre) breeding programs.

scholarly journals Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

2020 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Region Of Origin ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Genomic Regions ◽  
New Generation

AbstractVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity.Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

scholarly journals Portrait of a genus: the genetic diversity of Zea

2021 ◽  
Author(s):  
Lu Chen ◽  
Jingyun Luo ◽  
Minliang Jin ◽  
Ning Yang ◽  
Xiangguo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Flowering Time ◽  
Genetic Model ◽  
Genomic Variation ◽  
Model Organisms ◽  
Nucleotide Polymorphisms ◽  
Indel Polymorphisms ◽  
In The Wild ◽  
Modern Breeding ◽  
Direct Use

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

scholarly journals Selection for Tuber Characters Can Maintain High Specific Gravity in a Diploid Potato Breeding Population

HortScience ◽  
1990 ◽  
Vol 25 (2) ◽  
pp. 227-228 ◽  
Author(s):  
K.G. Haynes ◽  
F.L. Haynes
Keyword(s):  
Specific Gravity ◽  
Recurrent Selection ◽  
Breeding Population ◽  
High Specific Gravity ◽  
Solarium Tuberosum ◽  
Hybrid Population ◽  
Base Population ◽  
Diploid Potato Breeding ◽  
Growing Conditions ◽  
Tuber Specific Gravity

A base population of high specific gravity clones was established from a diploid hybrid population of Solarium tuberosum Group Phureja and Solarium tuberosum Group Stenotomum previously adapted to the long-day growing conditions in North Carolina. This base population was subjected to two 2-year cycles of recurrent selection. During each cycle, selections in the field were made on the basis of tuber smoothness, shape, and size. Tubers from unselected clones were bulked by plots. Tuber specific gravity was determined for the selected and unselected (bulk) clones. Tuber specific gravity was significantly greater in the selected than in the unselected clones in each cycle of selection.

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