Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density

2006 ◽  
Vol 62 (4) ◽  
pp. 175-189 ◽  
Author(s):  
Hui Wang ◽  
Chia-Ho Lin ◽  
Susan Service ◽  
Yuguo Chen ◽  
Nelson Freimer ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Marker Density ◽  
High Marker Density

scholarly journals Genotyping marker density reduction is not an effective approach in long-term prediction-based breeding of cross-pollinated crops

2021 ◽  
Author(s):  
Julio Cesar DoVale ◽  
Humberto Fanelli Carvalho ◽  
Felipe Sabadin ◽  
Roberto Fritsche-Neto
Keyword(s):  
Recurrent Selection ◽  
Computational Time ◽  
Marker Density ◽  
Additive Variance ◽  
Density Reduction ◽  
High Marker Density ◽  
Allogamous Species ◽  
Long Term Prediction ◽  
Density Marker

Abstract Reductions of genotyping marker density have been extensively evaluated as potential strategies to reduce the genotyping costs of genomic selection (GS). Low-density marker panels are appealing in GS because they entail lower multicollinearity and computational time-consumption and allow more individuals to be genotyped for the same cost. However, statistical models used in GS are usually evaluated with empirical data, using "static" training sets and populations. This may be adequate for making predictions during a breeding program's initial cycles, but not for the long term. Moreover, to the best of our knowledge, no GS models consider the effect of dominance, which is particularly important for breeding outcomes in cross-pollinated crops. Hence, dominance effects are an important and unexplored issue in GS for long-term programs involving allogamous species. To address it, we employed two approaches: analysis of empirical maize datasets and simulations of long-term breeding applying phenotypic and genomic recurrent selection (intrapopulation and reciprocal schemes). In both schemes, we simulated twenty breeding cycles and assessed the effect of marker density reduction on the population mean, the best crosses, additive variance, selective accuracy, and response to selection with models (additive, additive-dominant, general (GCA), and specific combining ability (SCA)). Our results indicate that marker reduction based on linkage disequilibrium levels provides useful predictions only within a cycle, as accuracy significantly decreases over cycles. In the long-term, high-marker density provides the best responses to selection. The model to be used depends on the breeding scheme: additive for intrapopulation and additive-dominant or SCA for reciprocal.

scholarly journals High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus

2019 ◽  
Vol 223 (3) ◽  
pp. 1489-1504 ◽  
Author(s):  
David Kainer ◽  
Amanda Padovan ◽  
Joerg Degenhardt ◽  
Sandra Krause ◽  
Prodyut Mondal ◽  
...  
Keyword(s):  
Oil Yield ◽  
Marker Density ◽  
Genomic Architecture ◽  
High Marker Density

scholarly journals An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

2018 ◽  
Author(s):  
Ranjana Bhattacharjee ◽  
Christian O Nwadili ◽  
Christopher A Saski ◽  
Agre Paterne ◽  
Brian E. Scheffler ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Average Score ◽  
Dioscorea Alata ◽  
Marker Density ◽  
Linkage Groups ◽  
Anthracnose Disease ◽  
High Marker Density ◽  
Water Yam

AbstractWater yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloesporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. A total of 380 EST-SSRs were used to generate a saturated linkage map. About 60.19% of SSRs showed Mendelian segregation pattern, however, it had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups covering a total length of 2559.66 cM, which agrees with the diploid nature (2n = 2x = 20) of the parents used in the cross. Majority of the markers were mapped on linkage group 1 comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporoides from West Africa. Using the mean permutation value of LOD scores as threshold value for declaring a putative QTL on all linkage groups, one QTL was consistently observed on linkage group (LG) 14 in all the three years and average score data. This QTL was found at position interval of 71.12 – 84.76 cM explaining 68.94% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.

scholarly journals Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

2021 ◽  
Author(s):  
Henrik Christiansen ◽  
Franz M. Heindler ◽  
Bart Hellemans ◽  
Quentin Jossart ◽  
Francesca Pasotti ◽  
...  
Keyword(s):  
Genome Size ◽  
Fine Tuning ◽  
Alternative Methods ◽  
Model Organisms ◽  
Restriction Enzyme Digestion ◽  
Marker Density ◽  
Reduced Representation ◽  
A Genome ◽  
High Marker Density ◽  
Reduced Representation Sequencing

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

scholarly journals Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Henrik Christiansen ◽  
Franz M. Heindler ◽  
Bart Hellemans ◽  
Quentin Jossart ◽  
Francesca Pasotti ◽  
...  
Keyword(s):  
Genome Size ◽  
Fine Tuning ◽  
Alternative Methods ◽  
Model Organisms ◽  
Restriction Enzyme Digestion ◽  
Marker Density ◽  
Reduced Representation ◽  
A Genome ◽  
High Marker Density ◽  
Reduced Representation Sequencing

Abstract Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

HIGH MARKER DENSITY AROUND THE PEACH NEMATODE RESISTANCE GENES

2004 ◽  
pp. 567-571 ◽  
Author(s):  
P. Arús ◽  
M. Mnejja ◽  
D. Esmenjaud ◽  
N. Bosselut ◽  
E. Dirlewanger
Keyword(s):  
Resistance Genes ◽  
Nematode Resistance ◽  
Marker Density ◽  
High Marker Density
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