Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

JL Fierst - Frontiers in genetics, 2015 - frontiersin.org
Modern high-throughput DNA sequencing has made it possible to inexpensively produce
genome sequences, but in practice many of these draft genomes are fragmented and …

High‐resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly

J Bartholomé, E Mandrou, A Mabiala, J Jenkins… - New …, 2015 - Wiley Online Library
Genetic maps are key tools in genetic research as they constitute the framework for many
applications, such as quantitative trait locus analysis, and support the assembly of genome …

Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models

M Mollinari, AAF Garcia - G3: Genes, Genomes, Genetics, 2019 - academic.oup.com
Modern SNP genotyping technologies allow measurement of the relative abundance of
different alleles for a given locus and consequently estimation of their allele dosage …

[HTML][HTML] Sugarcane genetics: Underlying theory and practical application

H Wang, YB Pan, M Wu, J Liu, S Yang, Q Wu, Y Que - The Crop Journal, 2024 - Elsevier
Sugarcane is recognized as the fifth largest crop globally, supplying 80% of sugar and 40%
of bioenergy production. However, sugarcane genetic research has significantly lagged …

High‐density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

C Plomion, J Bartholomé, I Lesur… - Molecular Ecology …, 2016 - Wiley Online Library
Maritime pine provides essential ecosystem services in the south‐western M editerranean
basin, where it covers around 4 million ha. Its scattered distribution over a range of …

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

C Bernhardsson, A Vidalis, X Wang… - G3: Genes …, 2019 - academic.oup.com
Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and
ecological importance. In common with most conifers, the P. abies genome is very large (∼ …

QTL Mapping of Growth-Related Traits in a Full-Sib Family of Rubber Tree (Hevea brasiliensis) Evaluated in a Sub-Tropical Climate

LM Souza, R Gazaffi, CC Mantello, CC Silva… - PLoS …, 2013 - journals.plos.org
The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary
plant used in natural rubber production. Due to genetic and physiological constraints, inbred …

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions

ARO Conson, CH Taniguti, RR Amadeu… - Frontiers in plant …, 2018 - frontiersin.org
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide
and has been extended to areas with suboptimal climates and lengthy drought periods; this …

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

AC Palhares, TB Rodrigues-Morais, MA Van Sluys… - Bmc Genetics, 2012 - Springer
Background The development of sugarcane as a sustainable crop has unlimited
applications. The crop is one of the most economically viable for renewable energy …

Molecular polymorphism and linkage analysis in sweet passion fruit, an outcrossing species

GS Pereira, ES Nunes, LDC Laperuta… - Annals of applied …, 2013 - Wiley Online Library
One of the current challenges of tropical fruit crop improvement is to incorporate molecular
marker‐based approaches into conventional breeding programmes. This study was …