High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

Abstract

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.

Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus

“…Most studies investigating important agronomic traits in B. napus were conducted with lower-density genetic maps67891011 and some with high-density linkage maps252629, but QTL analyses of SOC and SPC simultaneously based on high-density linkage maps have not been reported. In this study, we constructed a high-density integrated genetic linkage map with 3106 SNP and 101 non-SNP (SSR and STS) markers covering 3072.7 cM of the KNDH population.…”

“…In addition, the genomic sequences of the parental cultivars were also unknown in most of the previous studies, which also complicated the identification and analysis of candidate genes. Recent innovations in genome sequencing technology and bioinformatics and single nucleotide polymorphism (SNP) markers, especially the 60 K SNP Infinium Array, have been developed and widely applied for QTL mapping and the genetic dissection of important agronomical traits in B. napus 25262728293031. Simultaneously, the reference genome of B. napus has been released32, making it feasible to perform a comparative genome analysis between the genetic map and the physical map using SNPs with sequence information.…”

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

“…Among various molecular markers, SNPs represent the most abundant form of genetic variation. The availability of SNP data has increased the ability to analyze diversity in germplasm collections (van Treuren and van Hintum ; Mason et al ; Li and Erpelding ) and to make advances in plant breeding programs (Varshney et al ; Rafalski ; Fang et al ; Thomson ; Gao et al ; Wang et al ). The first SNP chip for cotton, the CottonSNP63K array (Illumina, USA), was developed in 2015, allowing assays for 45,104 putative intra‐specific SNP markers for use within the cultivated cotton species G. hirsutum L. and 17,954 putative inter‐specific SNP markers for use with crosses of other cotton species with G. hirsutum (Hulse‐Kemp et al ).…”

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

“…Moreover, many traits of agronomic importance in B. napus , such as seed coat color, oil content, and seed yield, are quantitative with complex genetic bases. Recently, a high-density linkage map was constructed using the Brassica 60 K Infinium BeadChip Array (Zou et al, 2012; Delourme et al, 2013; Liu et al, 2013; Zhang et al, 2014; Wang et al, 2015). Genome-specific SSR markers have been widely used for genetic mapping, association mapping, comparative mapping, QTL analysis, and marker-assisted selection (Li et al, 2011).…”