Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus.
Alleles
Binding Sites
/ genetics
Brassica napus
/ genetics
Chromosome Mapping
/ methods
Chromosomes, Plant
/ genetics
DNA Restriction Enzymes
/ metabolism
Flowers
/ genetics
Genes, Plant
/ genetics
Genome, Plant
/ genetics
Genotype
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
/ genetics
Sequence Analysis, DNA
/ methods
Time Factors
Brassica napus
Double digest restriction-site associated DNA sequencing
Flowering
QTL
SNP
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
07 Dec 2020
07 Dec 2020
Historique:
received:
16
07
2020
accepted:
25
11
2020
entrez:
8
12
2020
pubmed:
9
12
2020
medline:
14
9
2021
Statut:
epublish
Résumé
Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F
Sections du résumé
BACKGROUND
BACKGROUND
Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F
RESULTS
RESULTS
Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC.
CONCLUSIONS
CONCLUSIONS
These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F
Identifiants
pubmed: 33287721
doi: 10.1186/s12870-020-02756-y
pii: 10.1186/s12870-020-02756-y
pmc: PMC7720618
doi:
Substances chimiques
DNA Restriction Enzymes
EC 3.1.21.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
546Subventions
Organisme : Australian Research Council
ID : LP160100030
Organisme : Australian Research Council
ID : LP140100537
Organisme : Australian Research Council
ID : LP130100925
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