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

Yan, Tao; Wang, Qian; Maodzeka, Antony; Wu, Dezhi; Jiang, Lixi

doi:10.1016/j.csbj.2020.09.031

Cited by 18 publications

(6 citation statements)

References 25 publications

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“…GWAS is a commonly used method for identifying candidate genes associated with specific agronomic traits. Recent advancements in sequencing technology have significantly enhanced the efficiency of GWAS by providing a vast number of SNPs (Yan et al., 2020; Yang, He, et al., 2022; Yang, Liang, et al., 2022). Utilizing this technology to find associated genes comes with certain limitations, such as the requirement for a diverse genetic background in the population and significant variations in petal size across individuals.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association study reveals the genetic basis for petal‐size formation in rapeseed (Brassica napus) and CRISPR‐Cas9‐mediated mutagenesis of BnFHY3 for petal‐size reduction

Wang,

Li,

et al. 2023

The Plant Journal

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SUMMARYPetals in rapeseed (Brassica napus) serve multiple functions, including protection of reproductive organs, nutrient acquisition, and attraction of pollinators. However, they also cluster densely at the top, forming a thick layer that absorbs and reflects a considerable amount of photosynthetically active radiation. Breeding genotypes with large, small, or even petal‐less varieties, requires knowledge of primary genes for allelic selection and manipulation. However, our current understanding of petal‐size regulation is limited, and the lack of markers and pre‐breeding materials hinders targeted petal‐size breeding. Here, we conducted a genome‐wide association study on petal size using 295 diverse accessions. We identified 20 significant single nucleotide polymorphisms and 236 genes associated with petal‐size variation. Through a cross‐analysis of genomic and transcriptomic data, we focused on 14 specific genes, from which molecular markers for diverging petal‐size features can be developed. Leveraging CRISPR‐Cas9 technology, we successfully generated a quadruple mutant of Far‐Red Elongated Hypocotyl 3 (q‐bnfhy3), which exhibited smaller petals compared to the wild type. Our study provides insights into the genetic basis of petal‐size regulation in rapeseed and offers abundant potential molecular markers for breeding. The q‐bnfhy3 mutant unveiled a novel role of FHY3 orthologues in regulating petal size in addition to previously reported functions.

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Section: Discussionmentioning

confidence: 99%

Genome‐wide association study reveals the genetic basis for petal‐size formation in rapeseed (Brassica napus) and CRISPR‐Cas9‐mediated mutagenesis of BnFHY3 for petal‐size reduction

Wang,

Li,

et al. 2023

The Plant Journal

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“…First, abundant genomic information is available for Brassica and Brassicaceae germplasm, including high‐quality reference genomes (Table S2 ), organelle genomes (Mohd Saad et al ., 2021 ), pangenomes (Golicz et al ., 2016 ; Hurgobin et al ., 2018 ; Song et al ., 2020 ), gene annotations, transcriptomes, and high‐throughput genotypes for thousands of cultivars and breeding lines that have been identified by SNP chips and sequencing approaches (An et al ., 2019 ; Cheng et al ., 2016 ; Lu et al ., 2019 ; Schmutzer et al ., 2015 ; Wu et al ., 2018 ; Zhang et al ., 2017c ). These data were stored in public platforms for sharing and remaining including the Brassica Database ( http://39.100.233.196 ), the Brassica napus Genome Browser ( https://wwwdev.genoscope.cns.fr/brassicanapus/ ) (Chalhoub et al ., 2014 ), BnPedigome ( http://ibi.zju.edu.cn/bnpedigome/index.php ) (Zou et al ., 2019 ), BnaSNPDB ( http://rapeed.zju.edu.cn:3838/bnasnpdb ) (Yan et al ., 2020 ), and BnPIR ( http://cbi.hzau.edu.cn/bnapus/ ) (Song et al ., 2021b ). High‐throughput genotyping by whole‐genome sequencing, target segment sequencing and SNP‐chip array is ongoing for Brassica germplasm, and these data resources and genotyping techniques are becoming increasingly inexpensive and convenient for exploring Brassica pangenomic variation, and especially for identifying and introducing favourable genes and alleles into the B. napus gene pool.…”

Section: Challenges and Approaches For Further Exploring And Expanding The Rapeseed Gene Poolmentioning

confidence: 99%

Exploring the gene pool ofBrassica napusby genomics‐based approaches

Jing

Snowdon

et al. 2021

Plant Biotechnology Journal

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Summary De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population‐level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome‐sequencing projects. We also summarize progress in gene cloning, trait‐marker associations, gene editing, molecular marker‐assisted selection and genome‐wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic‐based improvement, as well as provide novel insights into the neo‐domestication of polyploid crops with novel genetic diversity from reconstructed genomes.

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“…Breeding efforts could be, therefore, focused on the transfer of restorer genes to a limited number of candidates, which are often achieved by backcrossing processes that usually take several years. To facilitate such applications, we established BnaSNPDB, an interactive web portal for efficient retrieval and analysis of Single Nucleotide Polymorphisms (SNPs) of 1,057 rapeseed germplasm accessions (https://bnapus-zju.com/ bnasnpdb) [34]. SNPs of a genotype can be easily retrieved for in silico pairing with SNPs of an Ogu-CMS-pool member to simulate hybrid vigor.…”

Section: Plos Geneticsmentioning

confidence: 99%

Prediction of heterosis in the recent rapeseed (Brassica napus) polyploid by pairing parental nucleotide sequences

et al. 2021

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The utilization of heterosis is a successful strategy in increasing yield for many crops. However, it consumes tremendous manpower to test the combining ability of the parents in fields. Here, we applied the genomic-selection (GS) strategy and developed models that significantly increase the predictability of heterosis by introducing the concept of a regional parental genetic-similarity index (PGSI) and reducing dimension in the calculation matrix in a machine-learning approach. Overall, PGSI negatively affected grain yield and several other traits but positively influenced the thousand-seed weight of the hybrids. It was found that the C subgenome of rapeseed had a greater impact on heterosis than the A subgenome. We drew maps with overviews of quantitative-trait loci that were responsible for the heterosis (h-QTLs) of various agronomic traits. Identifications and annotations of genes underlying high impacting h-QTLs were provided. Using models that we elaborated, combining abilities between an Ogu-CMS-pool member and a potential restorer can be simulated in silico, sidestepping laborious work, such as testing crosses in fields. The achievements here provide a case of heterosis prediction in polyploid genomes with relatively large genome sizes.

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

Abstract: Graphical abstract

Cited by 18 publications

References 25 publications

Genome‐wide association study reveals the genetic basis for petal‐size formation in rapeseed (Brassica napus) and CRISPR‐Cas9‐mediated mutagenesis of BnFHY3 for petal‐size reduction

Genome‐wide association study reveals the genetic basis for petal‐size formation in rapeseed (Brassica napus) and CRISPR‐Cas9‐mediated mutagenesis of BnFHY3 for petal‐size reduction

Exploring the gene pool ofBrassica napusby genomics‐based approaches

Prediction of heterosis in the recent rapeseed (Brassica napus) polyploid by pairing parental nucleotide sequences

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