Additional file 5: of Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Multiple sequence alignment of Aux/IAA genes in B. napus. Four conserved domains are indicated with black boxes. LxLxLx and GWPPv/i motifs in domain I and II are highlighted with black lines. The second LxLxLx motif between domain I and II is indicated with red boxes. NLSs and βαα motif are represented by black solid rectangles. The PB1 domain features of a conserved lysine and the OPCA-like motif phosphorylation sites are emphasized by black arrows (Korasick et al., Proc Natl Acad Sci USA, 2014(111): 5427–5432). (PDF 9716 kb

Manhattan and quantile-quantile plots of GWAS for seed oil content.

<p>The BLUP values of oil content across three years were used as phenotypes in GWAS. <b>(A)</b> Manhattan plot for oil content. The dashed horizontal line indicates the Bonferroni-adjusted significance threshold (<i>P</i> = 9.7×10^-5). Red dots above the threshold indicate the significant SNPs for oil content. <b>(B)</b> Quantile-quantile plot for oil content.</p

Workflow of the modified UNEAK pipeline.

<p><b>(A)</b> Short reads are collapsed to form tags for each inbred line. <b>(B)</b> The tags from all inbred lines in the association panel are collapsed again. <b>(C)</b> The tags only from a single inbred line are removed as sequencing errors. Only tags from more than one inbred line are kept for further analysis. <b>(D)</b> Pairwise alignment is performed between any two tags to form networks with at most two mismatches on each end of PE reads. <b>(E)</b> By employing the parameter error tolerance rate (ETR), the error tags (shaded circles) are removed from networks. <b>(F)</b> Scoring of allelic tag pairs using a network as an example. Each tag in the network is scored as an allele. “+” and “-” represent the presence and absence of the corresponding allele in an inbred line and then tabulate for the association panel. <b>(G)</b> The co-occurrence or combination of any two alleles from a locus within a network formed a possible genotype. And a co-occurrence matrix containing all possible homozygous and heterozygous genotypes is created. <b>(H)</b> Allelic tag pairs are discriminated from complicated networks mixed with homologous tags using relative heterozygosity (<i>H</i>_<i>R</i>). The tag pairs with <i>H</i>_<i>R</i> smaller than the empirical value (0.2) are considered as the allelic tags and then genotyped for each inbred line.</p

Alignments between the LD-based linkage map and the <i>B</i>. <i>napus</i> reference genome.

<p>The horizontal axis represents the genetic position (cM) of the SNPs on the genetic linkage map based on the BnaNZDH population [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146383#pone.0146383.ref021" target="_blank">21</a>] and LD-based mapping. The vertical axis represents the physical position (Mb) according to the <i>B</i>. <i>napus</i> reference genome ‘Darmor-<i>bzh</i>’ [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146383#pone.0146383.ref020" target="_blank">20</a>].</p

LD decay in the A and C subgenomes in the 189 <i>B</i>. <i>napus</i> diverse lines.

<p>The black dots indicate the <i>r</i>^<i>2</i> values of all SNP pairs within chromosomes for each subgenome. The red curve represents a nonlinear function of <i>r</i>² against the SNP physical distance (Mb). The horizontal blue dash line indicates the estimated background level of LD (<i>r</i>² = 0.26).</p

The haplotype block associated with genes controlling glucosinolate content.

<p>The gray windows represent the haplotype block for the entire panel, and the black dots indicate the PIC values of the SNPs in these region. The red boxes and the corresponding text indicate the positions and names of the genes possibly associated with the forming of the haplotype block.</p

Genome-wide distribution of haplotype blocks for the entire panel and two groups in the association mapping panel.

<p><b>(A)</b> The heatmap above indicates LD distribution. The color density represents the average <i>r</i>² values of all SNP pairs in a sliding-window of 500 kb. The map below indicates the distribution of haplotype blocks with length > 100 kb. The gray color represents the background and the blue color indicates the haplotype blocks. <b>(B)</b> The distributions of different types of haplotype blocks for the P1 and P2 groups across each chromosome. Gray rectangles represent genomic regions that don’t contain any haplotype block. Red rectangles represent the P1-specific haplotype blocks and blue rectangles represent the P2-specific haplotype blocks. Orchid rectangles represent the common haplotype blocks with frequency difference ≤0.4, and black rectangles represent the group-preferential haplotype blocks with frequency difference >0.4.</p

Introduction

It is an introduction of CIFOR's research in Bulungan, Kalimantan with the Ministry of Forestry in Indonesia and ITTO. CIFOR's strategic research is focused on policy issues to enable more informed, productive, sustainable and equitable decisions about the management and use of forests. CIFOR works closely with ITTO and FORDA (the Forestry Research and Development Agency, Ministry of Forestry, Indonesia) as important strategic partners in the Bulungan model forest project phase 1, 1997-2001. The aim of the research is to carry out a systematic investigation of how to achieve forest sustainability for a 'large forest landscape' in the humid tropics, where diverse, rapidly changing and often conflicting land use demand exist. The specific objectives of the activities conducted with ITTO support are: 1) Assessment of the effect of reduced-impact logging (RIL) on biodiversity, conservation, ecology and socio-economics, 2) Assessment of rural development trends and future policy options including the effects of macro-level development activities on people dependent on the forest

Additional file 2: of Sequence variation and functional analysis of a FRIGIDA orthologue (BnaA3.FRI) in Brassica napus

Sequence variations and haplotypes of BnaA3.FRI in 30 B. napus. (XLSX 14 kb

DataSheet_1_Genome-wide detection of genotype environment interactions for flowering time in Brassica napus.pdf

Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in Brassica napus. Here, a total of 11,700,689 single nucleotide polymorphisms in 490 B. napus accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in Arabidopsis, were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as BnaFLCs, BnaFTs, BnaA02.VIN3, and BnaC09.PRR7, were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed B. napus varieties adapted to particular environments with optimized flowering time.</p