scholarly journals Context-Specific Genomic Selection Strategies Outperform Phenotypic Selection for Soybean Quantitative Traits in the Progeny Row Stage

Crop Science ◽  
2019 ◽  
Vol 59 (1) ◽  
pp. 54-67 ◽  
Author(s):  
Christopher J. Smallwood ◽  
Arnold M. Saxton ◽  
Jason D. Gillman ◽  
Hem S. Bhandari ◽  
Phillip A. Wadl ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Quantitative Traits ◽  
Phenotypic Selection ◽  
Selection Strategies ◽  
Selection For ◽  
Context Specific

scholarly journals Pea Breeding for Intercropping With Cereals: Variation for Competitive Ability and Associated Traits, and Assessment of Phenotypic and Genomic Selection Strategies

2021 ◽  
Vol 12 ◽  
Author(s):  
Paolo Annicchiarico ◽  
Nelson Nazzicari ◽  
Tommaso Notario ◽  
Cristina Monterrubio Martin ◽  
Massimo Romani ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Plant Height ◽  
Competitive Ability ◽  
Phenotypic Selection ◽  
Indirect Selection ◽  
Flowering Plant ◽  
Complete Suppression ◽  
Selection Strategies ◽  
A Genome ◽  
Selection For

Mixed stand (MS) cropping of pea with small-grain cereals can produce more productive and environment-friendly grain crops relative to pure stand (PS) crops but may require selection to alleviate the pea competitive disadvantage. This study aimed to assess the pea variation for competitive ability and its associated traits and the efficiency of four phenotypic or genomic selection strategies. A set of 138 semi-leafless, semi-dwarf pea lines belonging to six recombinant inbred line populations and six parent lines were genotyped using genotyping-by-sequencing and grown in PS and in MS simultaneously with one barley and one bread wheat cultivar in two autumn-sown trials in Northern Italy. Cereal companions were selected in a preliminary study that highlighted the paucity of cultivars with sufficient earliness for association. Pea was severely outcompeted in both years albeit with variation for pea proportion ranging from nearly complete suppression (<3%) to values approaching a balanced mixture. Greater pea proportion in MS was associated with greater total yield of the mixture (r ≥ 0.46). The genetic correlation for pea yield across MS and PS conditions slightly exceeded 0.40 in both years. Later onset of flowering and taller plant height at flowering onset displayed a definite correlation with pea yield in MS (r ≥ 0.46) but not in PS, whereas tolerance to ascochyta blight exhibited the opposite pattern. Comparisons of phenotypic selection strategies within or across populations based on predicted or actual yield gains for independent years indicated an efficiency of 52–64% for indirect selection based on pea yield in PS relative to pea yield selection in MS. The efficiency of an indirect selection index including onset of flowering, plant height, and grain yield in PS was comparable to that of pea yield selection in MS. A genome-wide association study based on 5,909 SNP markers revealed the substantial diversity of genomic areas associated with pea yield in MS and PS. Genomic selection for pea yield in MS displayed an efficiency close to that of phenotypic selection for pea yield in MS, and nearly two-fold greater efficiency when also taking into account its shorter selection cycle and smaller evaluation cost.

scholarly journals Substitution Rates Under Stabilizing Selection

Genetics ◽  
1987 ◽  
Vol 116 (3) ◽  
pp. 479-486
Author(s):  
Alan Hastings
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Quantitative Traits ◽  
Strong Dependence ◽  
Phenotypic Selection ◽  
Analytical Models ◽  
Stabilizing Selection ◽  
Substitution Rates ◽  
Quantitative Characters ◽  
Selection For

ABSTRACT Allelic substitutions under stabilizing phenotypic selection on quantitative traits are studied in Monte Carlo simulations of 8 and 16 loci. The results are compared and contrasted to analytical models based on work of M. Kimura for two and "infinite" loci. Selection strengths of S = 4Nes approximately four (which correspond to reasonable strengths of selection for quantitative characters) can retard substitution rates tenfold relative to rates under neutrality. An important finding is a strong dependence of per locus substitution rates on the number of loci.

scholarly journals Marker-assisted selection for quantitative traits

2011 ◽  
Vol 11 (spe) ◽  
pp. 50-55 ◽  
Author(s):  
Ivan Schuster
Keyword(s):  
Molecular Markers ◽  
Cost Reduction ◽  
Marker Assisted Selection ◽  
Quantitative Traits ◽  
Large Scale ◽  
Recurrent Selection ◽  
Phenotypic Selection ◽  
Breeding Programs ◽  
The Subject ◽  
Selection For

Although thousands of scientific articles have been published on the subject of marker-assisted selection (MAS) and quantitative trait loci (QTL), the application of MAS for QTL in plant breeding has been restricted. Among the main causes for this limited use are the low accuracy of QTL mapping and the high costs of genotyping thousands of plants with tens or hundreds of molecular markers in routine breeding programs. Recently, new large-scale genotyping technologies have resulted in a cost reduction. Nevertheless, the MAS for QTL has so far been limited to selection programs using several generations per year, where phenotypic selection cannot be performed in all generations, mainly in recurrent selection programs. Methods of MAS for QTL in breeding programs using self-pollination have been developed.

Recurrent Phenotypic Selection for Resistance to Brown Leaf Spot in Smooth Bromegrass 1

Crop Science ◽  
1986 ◽  
Vol 26 (3) ◽  
pp. 533-536 ◽  
Author(s):  
Clyde C. Berg ◽  
Robert T. Sherwood ◽  
Kenneth E. Zeiders
Keyword(s):  
Leaf Spot ◽  
Phenotypic Selection ◽  
Smooth Bromegrass ◽  
Brown Leaf Spot ◽  
Brown Leaf ◽  
Selection For

scholarly journals Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 210
Author(s):  
Sang V. Vu ◽  
Cedric Gondro ◽  
Ngoc T. H. Nguyen ◽  
Arthur R. Gilmour ◽  
Rick Tearle ◽  
...  
Keyword(s):  
Moisture Content ◽  
Genomic Selection ◽  
Shell Length ◽  
Prediction Accuracy ◽  
Genomic Information ◽  
Morphometric Traits ◽  
Shell Weight ◽  
Shell Width ◽  
Crassostrea Angulata ◽  
Selection For

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

Genomic Selection for the Traits Expressed after Pollination in Allogamous Plants

Crop Science ◽  
2014 ◽  
Vol 54 (4) ◽  
pp. 1448-1457 ◽  
Author(s):  
Shiori Yabe ◽  
Ryo Ohsawa ◽  
Hiroyoshi Iwata
Keyword(s):  
Genomic Selection ◽  
Selection For

scholarly journals Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

2021 ◽  
Vol 12 ◽  
Author(s):  
◽  
Aline Fugeray-Scarbel ◽  
Catherine Bastien ◽  
Mathilde Dupont-Nivet ◽  
Stéphane Lemarié
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Plant Species ◽  
Animal Species ◽  
Animal Breeding ◽  
Breeding Cycle ◽  
Breeding Programs ◽  
The Third ◽  
Wide Range ◽  
Selection For

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

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