Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Development of DNA markers for Slmlo1.1, a new mutant allele of the powdery mildew resistance gene SlMlo1 in tomato (Solanum lycopersicum)

Reductions in growth and quality due to powdery mildew (PM) disease cause significant economic losses in tomato production. Oidium neolycopersici was identified as the fungal species responsible for tomato PM disease in South Korea in the present study, based on morphological and internal transcribed spacer DNA sequence analyses of PM samples collected from two remote regions (Muju and Miryang). The genes involved in resistance to this pathogen in the tomato accession ‘KNU-12’ (Solanum lycopersicum var. cerasiforme) were evaluated, and the inheritance of PM resistance in ‘KNU-12’ was found to be conferred via simple Mendelian inheritance of a mutant allele of the PM susceptibility locus Ol-2 (SlMlo1). Full-length cDNA analysis of this newly identified mutant allele (Slmlo1.1) showed that a 1-bp deletion in its coding region led to a frameshift mutation possibly resulting in SlMlo1 loss-of-function. An alternatively-spliced transcript of Slmlo1.1 was observed in the cDNA sequences of ‘KNU-12’, but its direct influence on PM resistance is unclear. A derived cleaved amplified polymorphic sequence (dCAPS) and a high-resolution melting (HRM) marker were developed based on the 1-bp deletion in Slmlo1.1, and could be used for efficient marker-assisted selection (MAS) using ‘KNU-12’ as the source for durable and broad-spectrum resistance to PM.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion

MITE insertion polymorphism (MIP) analysis of 19 MITE families in the <i>Brassica</i> genome.

<p>The accessions used here: 1- <i>B. napus</i> (Tapidor), 2- <i>B. napus</i> (Ningyou 7), 3- <i>B. rapa</i> (Chiifu), 4- <i>B. rapa</i> (Kenshin), 5- <i>B. oleracea</i> (C1234), 6- <i>B. oleracea</i> (C1184), 7- <i>B. oleracea</i> (C1235), 8- <i>A. thaliana</i> (Columbia). M, molecular size marker. <i>Black</i> and <i>gray</i> arrowheads indicate the products with and without MITE insertion, respectively.</p

Differential distribution of MITE family members in <i>B. rapa</i> and <i>B. oleracea</i>.

<p>MITE families with intact members were used for <i>in silico</i> map construction on the 256 Mb <i>B. rapa</i> (A) and the 385 Mb <i>B. oleracea</i> (B) pseudo-chromosome sequences based on the physical positions. The physical position information for the MITE families of <i>B. rapa</i> and <i>B. oleracea</i> are listed in Table S3 and S4, respectively.</p

Identification of related empty sites by sequence comparison of MITE flanking regions with corresponding regions from <i>B. rapa</i> (A genome) or <i>B. oleracea</i> (C genome) homologs.

<p>The chromosome numbers and start positions of the sequences are indicated at the beginning of the sequence. TSD sequences are shown in bold.</p

MITE insertion introduced a new exon into the Bra016667 gene of <i>B. rapa</i>.

<p>(A) Dot-plot comparison of genomic regions of BraTo-9-inserted gene Bra016667 with its paralogs Bra026774, Bra026150 and orthologs (At1g15270, <i>TRANSLATION MACHINERY ASSOCIATED7</i>) and Bol038124, Bol029240 and Bol031556 from <i>B. rapa</i>, <i>A. thaliana</i>, and <i>B. oleracea</i>, respectively. (B) Comparison of exon arrays of the genes shown in (A). The MITE based neo-exon is indicated as a green bar. The exon arrays were determined based on similarity to the ortholog At1g15270.</p

Comparison of 29 genes harboring BraTo-9 fragments with their homologous genes.

a<p>MITE position and alignment information can be found in Table S3.</p>b<p>Triplicated paralogs of <i>B. rapa</i> and orthologs from <i>A. thaliana</i> and <i>B. oleracea</i> were identified from BRAD annotation information. Bold indicates the gene with BraTo-9 insertion.</p