Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice

Wu, Di; Guo, Zilong; Ye, Junli; Feng, Hui; Liu, Jianxiao; Chen, Guoxing; Zheng, Jingshan; Yan, Dongmei; Yang, Xiaoquan; Xiong, Xiong; Liu, Qian; Niu, Zhiyou; Doonan, John; Xiong, Lizhong; Yang, Wanneng

doi:10.1093/jxb/ery373

Cited by 68 publications

(44 citation statements)

References 42 publications

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“…To benefit more labs, it is important to decrease the unit cost associated with high-throughput phenotyping not only in the lab but also in the field (Hawkesford and Lorence, 2017). Another trend is to increase the number and quality of quantified traits, especially novel traits or those requiring labor-intensive and destructive measurement; i.e., tiller growth (Wu et al, 2019) or panicle development (Jhala and Thaker, 2015) by X-ray CT.…”

Section: Groundmentioning

confidence: 99%

“…Here, we focus on genetic studies that have directly benefited from mechanized phenotyping platforms (Table 2), both within the laboratory and in the field. The phenotypic data listed in Table 2 can be categorized into organ-/tissue-related traits (Leiboff et al, 2015;Wu et al, 2019), plant morphological and leaf architecture traits (Bac-Molenaar et al, 2015;Yang et al, 2015;Condorelli et al, 2018), root anatomical traits (Courtois et al, 2013;Shi et al, 2013;Xie et al, 2017), biomass-or growth-related traits (Busemeyer et al, 2013b;Muraya et al, 2017;Zhang et al, 2017), drought-and salinity responserelated traits (Honsdorf et al, 2014;Al-Tamimi et al, 2016;Guo et al, 2018a;Condorelli et al, 2018), and yield-related traits (Yang et al, 2014;Crowell et al, 2016;Zhou et al, 2019), which have been used in genetic mapping and are discussed in the following.…”

Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

“…Combing a high-throughput micro-CT-RGB imaging system and GWASs, rice tiller traits and tiller growth traits as well as plant traits of nine growth stages could be obtained, and a total of 402 significantly associated loci were identified. In addition, two loci containing associations with both vigor-related traits and yield were identified for the further studies (Wu et al, 2019).…”

Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

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Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

et al. 2020

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Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.

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Section: Groundmentioning

confidence: 99%

Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

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Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

et al. 2020

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“…Here we outline steps for the high-throughput µCT scanning of small (< 2 cm) fossils, meant to facilitate advanced exploration of museum collections and allow researchers with limited access to specialized facilities the opportunity to maximize their investments. In contrast to other high-throughput µCT methods that have focused on clinical evaluations 32,33 or automated phenotyping of laboratory strains (e.g., mice 34 , rice 35 , zebrafish 36 ), we concentrate on the practical arrangement of accessioned museum specimens so that each individual can be identified and labelled in the 3D volume, followed by long-term storage and archiving. We illustrate this method using vertebrate (reptile, amphibian and mammal) fossils from the paleontological collections of Queensland Museum, Australia, as part of a larger effort to identify changes in morphology and species assemblages over geological time.…”

Section: Introductionmentioning

confidence: 99%

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

Hipsley

Aguilar

Black

et al. 2020

Preprint

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AbstractHigh-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite its potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitising numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

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“…Another GWAS led to the identification of a TN-associated 200 kb size locus that included 32 canidate genes (Lu et al, 2015c ). Dozens of loci associated with both TN variation (Wu et al 2018 ) and tiller angle-variation (Dong et al 2016 ) were recently identified using different natural rice populations. Because TN is a complex trait and the genetic basis of tillering is not completely understood, more research is needed to fully understand the genetic architecture of rice TN variations and identify more loci associated with tiller numbers (LATNs) in diverse germplasms.…”

Section: Introductionmentioning

confidence: 99%

Dissection of the Genetic Architecture of Rice Tillering using a Genome-wide Association Study

Jiang

Wang

Yan

et al. 2019

Rice

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Background Rice tiller number (TN) is one of the most important components associated with rice grain yield. Around one hundred rice TN genes have been identified, but dissecting the genetic architecture of rice TN variations remains difficult because of its complex trait and control by both major genes and quantitative trait loci (QTLs). Results In this study, we used a subset of the rice diversity population II (S-RDP-II), genotyped with 700,000 single nucleotide polymorphisms (SNPs), to identify the loci associated with tiller number variations (LATNs) through a genome-wide association study (GWAS). The analysis revealed that 23 LATNs are significantly associated with TN variations. Among the 23 LATNs, eight are co-localized with previously cloned TN genes, and the remaining 15 LATNs are novel. DNA sequence analysis of the 15 novel LATNs led to the identification of five candidate genes using the accessions with extreme TN phenotypes. Genetic variations in two of the genes are mainly located in the promoter regions. qRT-PCR analysis showed that the expression levels of these two genes are also closely associated with TN variations. Conclusions We identified 15 novel LATNs that contribute significantly to the genetic variation of rice TN. Of these 15, the five identified TN-associated candidate genes will enhance our understanding of rice tillering and can be used as molecular markers for improving rice yield. Electronic supplementary material The online version of this article (10.1186/s12284-019-0302-1) contains supplementary material, which is available to authorized users.

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Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice

Abstract: Combining high-throughput micro-CT-RGB phenotyping with genome-wide association study reveals the genetic architecture of tiller development in the indica subpopulation of rice.

Cited by 68 publications

References 42 publications

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

Dissection of the Genetic Architecture of Rice Tillering using a Genome-wide Association Study

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