Shovelomics for phenotyping root architectural traits of rapeseed/canola (Brassica napus L.) and genome-wide association mapping

Arifuzzaman, Muhammad; Oladzad, Atena; McClean, Phillip E.; Rahman, Mukhlesur

doi:10.1007/s00438-019-01563-x

Cited by 33 publications

(21 citation statements)

References 64 publications

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“…Some of them have a high throughput and are used for genetic analysis. For example, digging up the roots in the soil [13] is a simple and high-throughput method, being applied for genome-wide association studies to isolate loci affecting root architectural traits in Brassica napus [14]. Other popular field methods, such as monolith, auger, profile wall, and glass wall methods [12], involve longer processing times.…”

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confidence: 99%

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

et al. 2020

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Background: X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required. Results: We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-weekold seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over 3 weeks. Conclusions: We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method 'RSAvis3D' and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.

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confidence: 99%

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

et al. 2020

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“…These 290 accessions stand for more than 97% genetic polymorphism of the 991-accessions population in terms of SNPs and InDels, the population was small though. Relative to previous GWASs in rapeseed [29,30,[53][54][55], the present study applied a much smaller number of genetic accessions which was easily treated for field replicates. However, the 2,705,480 SNPs, which were very high in number, allow a very powerful identification of tightly associated genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

Wang

Pak

et al. 2021

BMC Plant Biol

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Background Rapeseed (Brassica napus L.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC. Results We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identified BnaC07g30920D, a patatin-like lipase (PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7–6.2% reduction of SOCs. We performed in silico analysis to show a total of 40 PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes of Brassica napus. RNA-seq analysis unveiled that BnPTLs were preferentially expressed in reproductive tissues especially maturing seeds. Conclusions We identified BnaC07g30920D, a BnPTL gene, that was associated with SOC using GWAS and performed in silico analysis of 40 PTLs in Brassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization of BnPTL genes.

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“…napus of the world. In comparison with previously described GWASs, such as Arifuzzaman, Oladzadabbasabadi, McClean, and Rahman (), He et al (), Lu et al (), Wang et al () and Wu et al () and, the current approach involves a much smaller population that is easily handled for GWAS, but a very high SNP number (2705480), which lends power to the analysis and allows identification of tightly associated genes. Brassicaceae plants have a large variation in trichome formation across wild and cultivated species (Beilstein, Al‐Shehbaz, & Kellogg, ).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

Xuan

Yan

et al. 2019

Plant Cell & Environment

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Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome‐wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy‐ and glabrous‐leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy‐ and glabrous‐leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy‐leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous‐leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.

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Shovelomics for phenotyping root architectural traits of rapeseed/canola (Brassica napus L.) and genome-wide association mapping

Cited by 33 publications

References 64 publications

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

Genome‐wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

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