Genome‐Wide Association Study of Developing Leaves' Heat Tolerance during Vegetative Growth Stages in a Sorghum Association Panel

Abstract Background Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study. Results Using inclusive composite interval mapping, 8 QTLs accounting for 6.44–8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDWv3-1-1 and qRDW/SDWv3-1-1), 2 (qRBNv1-2-1), 4 (qSUAv1-4-1, qSUAv2-4-1, and qROVv2-4-1), and 10 (qTRLv1-10-1, qRBNv1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages. Conclusions This study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems.

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Genome-Wide Association Study on Root Traits Under Different Growing Environments in Wheat (Triticum aestivum L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.646712 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fengdan Xu ◽

Shulin Chen ◽

Xiwen Yang ◽

Sumei Zhou ◽

Junsen Wang ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Snp Array ◽

Root Traits ◽

Hydroponic Culture ◽

Genome Wide Association ◽

Growth Stages ◽

Genome Wide ◽

A Genome ◽

Pot Culture

Plant roots are critical for water and nutrient acquisition, environmental adaptation, and yield formation. Herein, 196 wheat accessions from the Huang-Huai Wheat Region of China were collected to investigate six root traits at seedling stage under three growing environments [indoor hydroponic culture (IHC), outdoor hydroponic culture (OHC), and outdoor pot culture (OPC)] and the root dry weight (RDW) under OPC at four growth stages and four yield traits in four environments. Additionally, a genome-wide association study was performed with a Wheat 660K SNP Array. The results showed that the root traits varied most under OPC, followed by those under both OHC and IHC, and root elongation under hydroponic culture was faster than that under pot culture. Root traits under OHC might help predict those under OPC. Moreover, root traits were significantly negatively correlated with grain yield (GY) and grains per spike (GPS), positively correlated with thousand-kernel weight (TKW), and weakly correlated with number of spikes per area (SPA). Twelve stable chromosomal regions associated with the root traits were detected on chromosomes 1D, 2A, 4A, 4B, 5B, 6D, and unmapped markers. Among them, a stable chromosomal interval from 737.85 to 742.00 Mb on chromosome 4A, which regulated total root length (TRL), was identified under three growing environments. Linkage disequilibrium (LD) blocks were used to identify 27 genes related to root development. Three genes TraesCS4A02G484200, TraesCS4A02G484800, TraesCS4A02G493800, and TraesCS4A02G493900, are involved in cell elongation and differentiation and expressed at high levels in root tissues. Another vital co-localization interval on chromosome 5B (397.72–410.88 Mb) was associated with not only RDW under OHC and OPC but also TKW.

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Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

10.1101/2020.06.11.145953 ◽

2020 ◽

Author(s):

Rhonda C. Meyer ◽

Kathleen Weigelt-Fischer ◽

Dominic Knoch ◽

Marc Heuermann ◽

Yusheng Zhao ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Vegetative Growth ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Temporal Dynamics ◽

Expression Patterns ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

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Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab186 ◽

2021 ◽

Author(s):

Matheus Baseggio ◽

Matthew Murray ◽

Di Wu ◽

Gregory Ziegler ◽

Nicholas Kaczmar ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Sweet Corn ◽

The United States ◽

Zinc Homeostasis ◽

Genome Wide Association ◽

Association Panel ◽

Elemental Profile ◽

Genome Wide ◽

Corn Kernels

Abstract Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. Additionally, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.

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Genome-wide association study of multiple traits linked to heat tolerance in emmer-derived hexaploid wheat genotypes

Molecular Breeding ◽

10.1007/s11032-021-01222-3 ◽

2021 ◽

Vol 41 (4) ◽

Author(s):

Smi Ullah ◽

Imtiaz A. S. Randhawa ◽

Richard Trethowan

Keyword(s):

Association Study ◽

Heat Tolerance ◽

Hexaploid Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Multiple Traits ◽

Wheat Genotypes ◽

Genome Wide

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Genome-wide association study on root traits under different cultivation patterns in wheat

10.21203/rs.3.rs-27846/v1 ◽

2020 ◽

Author(s):

Fengdan Xu ◽

Shulin Chen ◽

Xiwen Yang ◽

Sumei Zhou ◽

Xu Chen ◽

...

Keyword(s):

Association Study ◽

Root Development ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Snp Array ◽

Root Traits ◽

Hydroponic Culture ◽

Genome Wide Association ◽

Growth Stages ◽

Genome Wide

Abstract Background Roots are critical for water and nutrient acquisition, environmental adaptation and yield formation. Results Here, 196 accessions from Yellow and Huai Winter Wheat Region (YHW) of China were collected for investigating the performance of six root traits under three cultivation patterns—Indoor Hydroponic Culture (IHC), Outdoor Hydroponic Culture (OHC) and Outdoor Pot Culture (OPC) at different growth stages—for three consecutive years. In the same growth period, OPC root traits always varied greatly, followed by OHC and IHC. The correlation coefficients between IHC and OPC at stooling stage (SS) were lower (0.016 ~ 0.278) than those between OHC and OPC (0.29 ~ 0.378). Root traits were negatively correlated grain yield (GY), the canonical correlation coefficient between root traits and yield was the highest (0.232) at SS. Genome-wide association study (GWAS) was furtherly conducted by a wheat 660K SNP array. It was revealed that 1105 SNP loci were significantly associated with root traits. A co-localized chromosomal segment regulating total root length (TRL) was detected on chromosome 4A, spanning from 737.85 to 742.00 Mb, under different cultivation patterns at stooling stage. Another co-localization region regulating total root area (TRA) was detected on chromosome 5A, an approximately 6.17 ~ 18.76 Mb region at SS, wintering stage (WT) and jointing stage (JS) under OPC. LD analysis and blast comparison revealed 27 and 31 genes related to root development were found from these two segments, respectively. Among them, TraesCS4A02G493900, TraesCS4A02G494200, TraesCS5A02G021700, TraesCS5A02G021800 and TraesCS5A02G011600 were predicted to be highly expressed in root. Conclusion This work could deepen our understanding of the molecular mechanisms of root development under different cultivation patterns in common wheat.

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