Genome-wide association study and protein network analysis for understanding candidate genes involved in root development at the rapeseed seedling stage

He, Ying; Hu, Dingxue; You, Jingcan; Wu, Daoming; Cui, Yixin; Dong, Hongli; Li, Jiana; Qian, Wei

doi:10.1016/j.plaphy.2019.01.028

Cited by 11 publications

(4 citation statements)

References 55 publications

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“…Currently, association mapping has been widely used in the identification and genetic testing of important quantitative trait locus (QTL) in various species [6][7][8][9][10][11][12][13][14][15][16][17]. And some progress has been made in studies on crop yield.…”

Section: Introductionmentioning

confidence: 99%

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

Liu

Cheng

2020

BMC Plant Biol

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Background Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). Results The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). Conclusions Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.

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Section: Introductionmentioning

confidence: 99%

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

Liu

Cheng

2020

BMC Plant Biol

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“…Rapeseed absorbs between 290 to 373 kg ha −1 of K, with the majority of the K coming from the soil. Some studies in B. napus have focused on root traits, specifically the root development at the seedling stage; root vigor; root development at the mature stage; root growth dynamics; variations in root growth habits of spring, winter, and semi-winter rapeseed; and the significance of root morphology in terms of phosphorus and nitrogen absorption [35][36][37][38][39][40][41][42][43]. So far, few studies have identified genetic pathways or genes associated with the architecture of the root system in B. napus grown in low-potassium environments.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions

Ibrahim

Ahmad

Kuang

et al. 2022

Plants

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Roots are essential organs for a plant’s ability to absorb water and obtain mineral nutrients, hence they are critical to its development. Plants use root architectural alterations to improve their chances of absorbing nutrients when their supply is low. Nine root traits of a Brassica napus association panel were explored in hydroponic-system studies under low potassium (K) stress to unravel the genetic basis of root growth in rapeseed. The quantitative trait loci (QTL) and candidate genes for root development were discovered using a multilocus genome-wide association study (ML-GWAS). For the nine traits, a total of 453 significant associated single-nucleotide polymorphism (SNP) loci were discovered, which were then integrated into 206 QTL clusters. There were 45 pleiotropic clusters, and qRTA04-4 and qRTC04-7 were linked to TRL, TSA, and TRV at the same time, contributing 5.25–11.48% of the phenotypic variance explained (PVE) to the root traits. Additionally, 1360 annotated genes were discovered by examining genomic regions within 100 kb upstream and downstream of lead SNPs within the 45 loci. Thirty-five genes were identified as possibly regulating root-system development. As per protein–protein interaction analyses, homologs of three genes (BnaC08g29120D, BnaA07g10150D, and BnaC04g45700D) have been shown to influence root growth in earlier investigations. The QTL clusters and candidate genes identified in this work will help us better understand the genetics of root growth traits and could be employed in marker-assisted breeding for rapeseed adaptable to various conditions with low K levels.

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“…Intensive genetic studies have been led to the identification of numerous QTLs and the relative genes underlying the genetic control of different root traits in rice (Chen et al 2013 ; Uga et al 2015 ; Han et al 2018 ; Ramanathan et al 2018 ; He et al 2019 ; Sandhu et al 2019 ). However, phenotyping of root structural traits is difficult and laborious to implement and constitutes the main bottleneck in using genomics approaches.…”

Section: Introductionmentioning

confidence: 99%

Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?

Guimarães

Lima

Castro

et al. 2020

Rice

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Background The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology. Results High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought. Conclusions This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.

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Genome-wide association study and protein network analysis for understanding candidate genes involved in root development at the rapeseed seedling stage

Cited by 11 publications

References 55 publications

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions

Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?

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