Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata

Abstract

An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time. An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq(TM) markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.

Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata

“…Compared to other traits investigated in this study, only flowering time was determined in three different contrasting environments. We reanalyzed QTL for flowering time that were determined in a previous study (Zou et al, 2014), with the data collected from Australian Spring environment (WW13 and WW14).…”

“…A genetic linkage map of the doubled haploid (DH) population (named as YW population) derived from a cross between two DH accessions of B. carinata , Y-BcDH64 (yellow petal) and W-BcDH76 (white petal), was constructed using a total of 212 amplified fragment length polymorphism (AFLP), intron based polymorphism (IBP), sequence-related amplified polymorphism (SRAP), and simple sequence repeats (SSR) markers, and covered 1,703 cM with a marker density of 8 cM between adjacent loci (Guo et al, 2012). In addition, a high density genetic linkage map of the YW DH population integrating existing 212 markers (Guo et al, 2012) and 3,819 presence-absence markers based on genotyping-by-sequencing, DArTseq markers (the traditional DArT and next-generation sequencing technique called DArTseq, Raman et al, 2014), was established with increasing genome-wide coverage (2,048 cM) (Zou et al, 2014). The genetic map of YW DH population was subsequently used for the QTL mapping of genetic loci involved in petal color, another tip color, seed coat color (Guo et al, 2012), and flowering and budding time (Zou et al, 2014).…”

“…In addition, a high density genetic linkage map of the YW DH population integrating existing 212 markers (Guo et al, 2012) and 3,819 presence-absence markers based on genotyping-by-sequencing, DArTseq markers (the traditional DArT and next-generation sequencing technique called DArTseq, Raman et al, 2014), was established with increasing genome-wide coverage (2,048 cM) (Zou et al, 2014). The genetic map of YW DH population was subsequently used for the QTL mapping of genetic loci involved in petal color, another tip color, seed coat color (Guo et al, 2012), and flowering and budding time (Zou et al, 2014). However, a limited phenotypic datasets especially on agronomic traits were available for QTL detection and routine marker-assisted selection.…”

Induction of parthenogenetic haploid plants using gamma irradiated pollens in ‘Hirado Buntan’ pummelo (Citrus grandis [L.] Osbeck)

“…Homozygous genotypes, which are of great value in genetic and genomic researches in higher plants (Dunwell, 2010;Dwivedi et al, 2015), have been widely applied in QTLs (Zou et al, 2014;Ye et al, 2015), linkage mapping studies (Aleza et al, 2009), and particularly in genome sequencing in recent years due to their significant advantage in fragment assembly (Argout et al, 2011;The international Peach Genome Initiative, 2013). Homozygous lines can also be extensively applied in producing novel germplasm resources, such as triploid breeding via somatic fusion (Kobayashi et al, 1997;Ollitrault and Dambier, 2008).…”

Introgressing Subgenome Components from Brassica rapa and B. carinata to B. juncea for Broadening Its Genetic Base and Exploring Intersubgenomic Heterosis

“…The synthesis of the SSR primers, conditions for PCR, and processing of the data generated by capillary sequencing were all described previously (Chen et al, 2010) using an AB3730xl capillary sequencer (Applied Biosystems, USA). An additional set of SSR markers anchored on 31 loci from the B genome in B. carinata (Zou et al, 2014) was used to evaluate the introgression of B genomic components (Supplementary Table 3). The markers were scored according to the polymorphism appeared in the parents and population.…”