Designing of a mini-core that effectively represents 3004 diverse accessions of rice

Kumar, Angad; Kumar, Shivendra; Prasad, Manoj; Thakur, Jyoti

doi:10.1101/762070

Cited by 2 publications

(4 citation statements)

References 47 publications

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“…Previously known major seed length (GS3) and width (qSW5) regulators are highlighted with a red arrow. the significant SNP on chromosome 5 (SNP5.5348012; -log 10 P = 5.56; see Figure 6 and Supplementary Table S10) corresponded to a known regulator for seed width, qSW5/GW5 (Weng et al, 2008;Duan et al, 2017;Liu et al, 2017;Kumar et al, 2019). This SNP explained phenotypic variation of 4.4%, which is in line with the previous studies (Huang et al, 2010;Zhao et al, 2011).…”

Section: Validation Of Seedextractor Derived Morphometric and Colorimetric Datasupporting

confidence: 85%

“…For instance, the lead SNP on chromosome 2 (SNP2.2487459; -log 10 P = 6.07) co-localizes with an expressed protein ( Os02g05199 ), and the SNP on chromosome 3 (SNP3.10130641; -log 10 P = 5.84) is localized in the intergenic sequence between Os03g18130 and Os03g18140 (see Figure 6 and Supplementary Table S10 ). Interestingly, the significant SNP on chromosome 5 (SNP5.5348012; -log 10 P = 5.56; see Figure 6 and Supplementary Table S10 ) corresponded to a known regulator for seed width, qSW5/GW5 ( Weng et al, 2008 ; Duan et al, 2017 ; Liu et al, 2017 ; Kumar et al, 2019 ). This SNP explained phenotypic variation of 4.4%, which is in line with the previous studies ( Huang et al, 2010 ; Zhao et al, 2011 ).…”

Section: Resultsmentioning

confidence: 99%

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SeedExtractor: An Open-Source GUI for Seed Image Analysis

et al. 2021

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Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.

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Section: Validation Of Seedextractor Derived Morphometric and Colorimetric Datasupporting

confidence: 85%

Section: Resultsmentioning

confidence: 99%

SeedExtractor: An Open-Source GUI for Seed Image Analysis

et al. 2021

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“…The lead SNP (chr5.5348012) underlying this peak explained 4.1% and 6.3% of phenotypic variation under control and HNT conditions, respectively (Table S4). The phenotypic variation explained by this lead SNP is similar to the phenotypic variation detected for the same SNP from previous studies (Huang et al ., 2010; Zhao et al ., 2011), and this SNP corresponds to qSW5/GW5 , that is, a known regulator for grain width (Weng et al ., 2008; Duan et al ., 2017; Liu et al ., 2017; Kumar et al ., 2019). Another significant SNP for grain width that was stronger under HNT was detected on chr 8.…”

Section: Resultsmentioning

confidence: 99%

“…New Phytologist (2021) 229: 335-350 Ó 2020 The Authors New Phytologist Ó 2020 New Phytologist Trust www.newphytologist.com (Weng et al, 2008;Duan et al, 2017;Liu et al, 2017;Kumar et al, 2019). Another significant SNP for grain width that was stronger under HNT was detected on chr 8.…”

Section: Phenotypic Variation For Grain Size Under Hnt Stressmentioning

confidence: 99%

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

et al. 2020

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A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response of Fie1 in grains developing under HNT stress. We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

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Designing of a mini-core that effectively represents 3004 diverse accessions of rice

Abstract: One-sentence summary:Designing of mini-core as manageable association panel that efficiently mirroring the large and diverse collection of 3004 rice accessions.

Cited by 2 publications

References 47 publications

SeedExtractor: An Open-Source GUI for Seed Image Analysis

SeedExtractor: An Open-Source GUI for Seed Image Analysis

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

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