Genetic and Genomic Resources to Study Natural Variation in<i>Brassica rapa</i>

Lou, Ping; Woody, Scott; Greenham, Kathleen; VanBuren, Robert; Colle, Marivi; Edger, Patrick P.; Sartor, Ryan C.; Yining, Zheng; Levendoski, Nathan; Lim, Jan; So, Calvin; Stoveken, Brian; Woody, Timothy; Jian-jun, Zhao; Shen, Shuxing; Amasino, Richard M.; McClung, C Robertson

doi:10.1101/2020.06.23.167270

Cited by 4 publications

(6 citation statements)

References 49 publications

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“…We identified syntenic homologous genes (syntelogs) between Brassica rapa (IMB218 SNP-corrected, R500 reference genome; Lou et al 2020) and Brassica oleracea (TO1000; Parkin et al 2014) reference genomes with the MCScan toolkit (Tang et al, 2008). For the synthetic polyploid these represent as syntenic homoeologs.…”

Section: Wgs Analysismentioning

confidence: 99%

“…An individual from six resynthesized lines was sequenced at the first (S1), fifth (S5), and tenth selfing generation (S10) and we analyzed the genomes of these 18 individuals to examine if changes in gene (homoeolog) dosage due to homoeologous exchanges are biased towards a particular subgenome. The genome sequencing data was aligned to an in silica allopolyploid genome made by combining the reference genomes of the B. oleracea double-haploid parent line TO1000 (Parkin et al 2014) and a parental-SNP corrected B. rapa R500 reference genome (Lou et al 2020). We identified 26,114 homoeologs between the BnA and BnC subgenomes by identifying syntenic orthologs between the progenitor B. oleracea and B. rapa genomes.…”

Section: Gene Dosage Changes Are Highly Variable and Do Not Show Signs Of Subgenome Biasmentioning

confidence: 99%

“…We SNP corrected the Brassica rapa R500 (Lou et al 2020) reference genome with paired-end 150-bp Illumina reads for the doubled haploid Brassica rapa accession IMB-218, using Bowtie2 v.2.3.4.1 (Langmead & Salzberg, 2012), Picardtools v.2.8.1. and GATK v.3.5.0.…”

Section: In Silico Reference Genome Constructionmentioning

confidence: 99%

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Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Bird

Pires

VanBuren

et al. 2021

Preprint

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Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Frequently, allopolyploids exhibit genomic rearrangements that recombine, duplicate, or delete homoeologous regions of the newly formed genome. While decades of investigation have focused on how genome duplication leads to systematic differences in the retention and expression of duplicate genes, the impact of genomic rearrangements on genome evolution has received less attention. We used genomic and transcriptomic data for six independently resynthesized, isogenic Brassica napus lines in the first, fifth, and tenth generation to identify genomic rearrangements and assess their impact on gene expression dynamics related to subgenome dominance and gene dosage constraint. We find that dosage constraints on the gene expression response to polyploidy begin to loosen within the first ten generations of evolution and systematically differ between dominant and non-dominant subgenomes. We also show that genomic rearrangements can bias estimation of homoeolog expression bias, but fail to fully obscure which subgenome is dominantly expressed. Finally, we demonstrate that dosage-sensitive genes exhibit the same kind of coordinated response to homoeologous exchange as they do for genome duplication, suggesting constraint on dosage balance also acts on these changes to gene dosage.

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Section: Wgs Analysismentioning

confidence: 99%

Section: Gene Dosage Changes Are Highly Variable and Do Not Show Signs Of Subgenome Biasmentioning

confidence: 99%

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Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Bird

Pires

VanBuren

et al. 2021

Preprint

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“…Considering the economic importance of B. rapa crops, their relationships and order of domestication have to be understood. In fact, several B. rapa crops have been investigated by phylogenetic and population genetics analyses 6 , 7 . Mizuna and Mibuna are intriguing targets to gain insights into the emergence of local-subspecies.…”

Section: Introductionmentioning

confidence: 99%

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

et al. 2021

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Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna.

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“…Up to now, classical forward genetics, such a linkage mapping and/or GWAS, helped to identify quantitative trait loci (QTLs) involved in both upstream (perception) and downstream mechanisms associated with plant resistance to insect feeding [15,[52][53][54][55][56]. Currently, genetic mapping efforts in Brassica species are increasingly made possible given a growing availability of high quality genomic and genetic resources [57][58][59][60]. It is thus timely to use genetic approaches to unravel the genetics underlying plant-insect egg interactions in non-model species.…”

Section: Introductionmentioning

confidence: 99%

Genetic Analysis Reveals Three Novel QTLs Underpinning a Butterfly Egg-Induced Hypersensitive Response-Like Cell Death in Brassica Rapa

Bassetti

Caarls

Bukovinszkine’Kiss

et al. 2021

Preprint

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Background Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa. Results A germplasm screening of B. rapa 56 accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 contains also LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract. Conclusions This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.

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Genetic and Genomic Resources to Study Natural Variation inBrassica rapa

Cited by 4 publications

References 49 publications

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

Genetic Analysis Reveals Three Novel QTLs Underpinning a Butterfly Egg-Induced Hypersensitive Response-Like Cell Death in Brassica Rapa

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