Genome‐wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

Abstract

Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome‐wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy‐ and glabrous‐leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy‐ and glabrous‐leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy‐leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous‐leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.

Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

“…To reveal natural variation of genomic sequences of GATA genes in B. napus, SNPs in the coding regions of GATA genes were determined in a worldwide collection of B. napus germplasm of 300 accessions in light of the genome re-sequencing data of our previous studies [26,27]. Highquality SNPs with MAF larger than 5% and missing rate less than 50% were used for the further analysis.…”

“…To date, the genomes of Darmor-bzh (winter ecotype), Tapitor (winter ecotype), Zhongshuang 11 were successfully sequenced and assembled [23][24][25]. Recently, we re-sequenced 991 accessions from the global rapeseed germplasm and established a worldwide core collection [26,27]. In this study, 96 GATA genes were identified and characterized in the genome of B. napus.…”

Genome-wide identification and characterization of SnRK family genes in Brassica napus

“…The polymorphism of BnSnRK genes was determined using our previous resequencing data of a core germplasm resource containing 300 accessions [29,30]. The SNPs with MAF more than 5% in BnSnRK genes were selected out (Table S9).…”

“…The SNPs in the coding regions of BnSnRK genes were extracted from the total SNPs of 300 B.napus accessions, which were determined by the genome re-sequencing in our previous studies [29,30]. High-quality SNPs with MAF greater than 5% and missing rate less than 50% were used for further analysis.…”

BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions

“…Therefore, in BnaSNPDB, the analyses were based on SNP variations. FLOWERING LOCUS C ( BnaA10g22080D ) [4] and SWEET4 ( BnaC07g24860D ) [20] were used as examples to show the associations between allelic SNP variations in genetic populations and agronomic traits, such as flowering time and leaf trichome, respectively, and to demonstrate the efficiency of the tools ( Fig. 2 A; Supplementary Fig.…”