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Annexins (ANN) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGCNA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia., (© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.)

Arabidopsis Transparent Testa Glabra 1 (TTG1) genes were cloned from three diploid Brassica species (B. rapa, B. nigra and B. oleracea) and two amphidiploids species (B. juncea and B. carinata) by homology cloning. TTG1 homologues identified in all the accessions of the investigated species had a coding sequence of 1,014 bp. One copy was obtained from each diploid species and two copies from each amphidiploid species. Combined analysis of the TTG1 sequences cloned in this study with those obtained from public databases demonstrated that three, forty-five and seven nucleotides were specific variations in TTG1 genes from genomes A, B and C, respectively. Primers designed with genome-specific nucleotide variations were able to distinguish among TTG1 genes originating from genomes A, B and C in Brassica. Therefore, the TTG1 gene could serve as a candidate marker gene to detect the pollen flow of Brassica and provide an alternative method for the detection of pollen drift and risk assessment of gene flow in Brassica species.

Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed. [ABSTRACT FROM AUTHOR]

Sclerotinia rot is a fungal disease caused by Sclerotinia sclerotiorum (Lib.) de Bary, which has severely reduced rapeseed production worldwide. Polygalacturonase-inhibiting proteins (PIGPs) inhibit the activity of polygalacturonases, which are secreted during fungal infection in plants. This study investigated the function of the polygalacturonase-inhibitor gene 2 ( PGIP2) in sclerotinia rot resistance. The PGIP2 was successfully expressed in a prokaryotic system, and recombinant PGIP2 protein, purified after enterokinase treatment to remove tag peptide, inhibited S. sclerotiorum PG activity in vitro. PGIP2 was overexpressed in the susceptible Brassica napus cultivar 98c40 via Agrobacterium-mediated transformation. After inoculation with S. sclerotiorum mycelia, the transgenic rapeseed demonstrated greatly reduced leaf damage, as compared with their non-transgenic plants. Therefore, the PGIP2 encodes a functional protein and would be a candidate gene for enhancing Sclerotinia rot resistance. [ABSTRACT FROM AUTHOR]

Anthocyanidin synthase (ANS) is a key enzyme of the proanthocyanidin biosynthetic pathway in Arabidopsis. In this study, we report cloning and characterization of an ANS homolog, BjANS, from Brassica juncea. The BjANS cDNA sequence is 1,377 bp long and has a 1,077-bp open reading frame encoding a deduced polypeptide of 358 amino acids with a predicted molecular weight of 40,862 Da and an estimated isoelectric point of 5.18. The putative BjANS protein shows 91-99% amino acid sequence identity with Arabidopsis thaliana, Matthiola incana, B. rapa and B. oleracea ANS proteins. The expression of BjANS was analyzed in yellow- and black-seeded B. juncea accessions to determine its physiological function. RT-PCR analysis showed that BjANS expressed in the seed coats of the black-seeded lines and in embryos of the all lines, but not in the yellow-seeded seed coats. Proanthocyanidins were also detected by histochemical analysis in the seed coat of black-seeded accessions and in embryos of all the lines, but not the yellow-seeded seed coat. Both transcriptional and histochemical analyses confirmed that BjANS was involved in the biosynthesis of proanthocyanidins and in seed coat color formation of B. juncea. Lack of BjANS expression blocked biosynthesis of proanthocyanidins in the yellow seed coat, and therefore seeds appeared yellow because of transparent testa. [ABSTRACT FROM AUTHOR]

• The GCA of 950 F1 hybrids from 475 spring-type canola pollinator lines crossed with two tester lines. • 24,403 single-copy, genome-wide SNP loci were employed using 60 K Brassica SNP Infinium Consortium array. • Eight and seven haplotype regions were detected significantly association with the GCA values for DTF and GSL, respectively. • Interactions between haplotypes producing low GSL and early flowering time in hybrid crosses were identified. • Reconstructed phased F1 hybrid genotypes from the beneficial parental haplotype alleles. Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs. [ABSTRACT FROM AUTHOR]