Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis [PDF]
G3 Genes|Genomes|Genetics, 2015 Abstract Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications ...
Tinker, Nicholas A +2 more
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Ecology and Evolution, 2021 Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent ...
Alejandro Llanos‐Garrido +2 more
doaj +1 more source
Selection Mapping Identifies Loci Underpinning Autumn Dormancy in Alfalfa (Medicago sativa). [PDF]
, 2018 Autumn dormancy in alfalfa (Medicago sativa) is associated with agronomically important traits including regrowth rate, maturity, and winter survival. Historical recurrent selection experiments have been able to manipulate the dormancy response.
Brummer, E Charles +3 more
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Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae) [PDF]
, 2019 A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns ...
Aparicio Martínez, Abelardo +7 more
core +1 more source
Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden
Agronomy, 2019 Restriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling.
Natalia Cristina Aguirre +14 more
doaj +1 more source
Genomic Prediction in Tetraploid Ryegrass Using Allele Frequencies Based on Genotyping by Sequencing
Frontiers in Plant Science, 2018 Perennial ryegrass is an outbreeding forage species and is one of the most widely used forage grasses in temperate regions. The aim of this study was to investigate the possibility of implementing genomic prediction in tetraploid perennial ryegrass, to ...
Xiangyu Guo +7 more
doaj +1 more source
Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions [PDF]
, 2019 Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant
Francisco, Felipe O. +6 more
core +2 more sources
Genotyping-by-sequencing and genomic selection applications in hexaploid triticale [PDF]
G3 Genes|Genomes|Genetics, 2021 Abstract Triticale, a hybrid species between wheat and rye, is one of the newest additions to the plant kingdom with a very short history of improvement. It has very limited genomic resources because of its large and complex genome. Objectives of this study were to generate dense marker data, understand genetic diversity, population ...
Habtamu Ayalew +7 more
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Wheat rusts never sleep but neither do sequencers: will pathogenomics transform the way plant diseases are managed? [PDF]
, 2015 Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host ...
Derevnina, Lida, Michelmore, Richard W
core +2 more sources
Construction of relatedness matrices using genotyping-by-sequencing data [PDF]
BMC Genomics, 2015 AbstractBackgroundGenotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality.
Dodds, Ken G +6 more
openaire +2 more sources