scholarly journals Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea

2018 ◽  
Vol 8 ◽  
Author(s):  
Aurore Desgroux ◽  
Valentin N. Baudais ◽  
Véronique Aubert ◽  
Gwenola Le Roy ◽  
Henri de Larambergue ◽  
...  
Keyword(s):  
Association Mapping ◽  
Root System ◽  
System Architecture ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Aphanomyces Euteiches ◽  
Comparative Genome ◽  
Genome Wide

scholarly journals Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

PLoS Genetics ◽  
2019 ◽  
Vol 15 (12) ◽  
pp. e1008126 ◽  
Author(s):  
Marco Giovannetti ◽  
Christian Göschl ◽  
Christof Dietzen ◽  
Stig U. Andersen ◽  
Stanislav Kopriva ◽  
...  
Keyword(s):  
Association Mapping ◽  
Root System ◽  
System Architecture ◽  
Lotus Japonicus ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Novel Genes ◽  
Phosphate Accumulation ◽  
Genome Wide

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Exploiting natural variation in crown root traits via genome-wide association studies in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Houmiao Wang ◽  
Xiao Tang ◽  
Xiaoyi Yang ◽  
Yingying Fan ◽  
Yang Xu ◽  
...  
Keyword(s):  
Root System ◽  
Candidate Genes ◽  
System Architecture ◽  
Root Traits ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Crown Root ◽  
Genome Wide ◽  
Maize Varieties

Abstract Background Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear. Methods In this study, the CRA, CRD, and CRN of 316 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using two single-locus methods (GLM and MLM) and three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA) with 140,421 SNP. Results A total of 38 QTL including 126 SNPs were detected for CRA, CRD, and CRN. Additionally, 113 candidate genes within 50 kb of the significant SNPs were identified. Combining the gene annotation information and the expression profiles, 3 genes including GRMZM2G141205 (IAA), GRMZM2G138511 (HSP) and GRMZM2G175910 (cytokinin-O-glucosyltransferase) were selected as potentially candidate genes related to crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN in different environments. Four haplotypes were detected based on these significant variants, and Hap1 has more CRN. Conclusions These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions.

scholarly journals Exploiting natural variation in root system architecture via genome-wide association studies

2020 ◽  
Vol 71 (8) ◽  
pp. 2379-2389 ◽  
Author(s):  
Agnieszka Deja-Muylle ◽  
Boris Parizot ◽  
Hans Motte ◽  
Tom Beeckman
Keyword(s):  
Root System ◽  
System Architecture ◽  
Association Studies ◽  
Root Traits ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Important Research Topic ◽  
Root Growth And Development

Abstract Root growth and development has become an important research topic for breeders and researchers based on a growing need to adapt plants to changing and more demanding environmental conditions worldwide. Over the last few years, genome-wide association studies (GWASs) became an important tool to identify the link between traits in the field and their genetic background. Here we give an overview of the current literature concerning GWASs performed on root system architecture (RSA) in plants. We summarize which root traits and approaches have been used for GWAS, mentioning their respective success rate towards a successful gene discovery. Furthermore, we zoom in on the current technical hurdles in root phenotyping and GWAS, and discuss future possibilities in this field of research.

Exploiting Natural Variation in Crown Root Traits via Genome-Wide Association Studies in Maize

2021 ◽  
Author(s):  
Houmiao Wang ◽  
Xiao Tang ◽  
Xiaoyi Yang ◽  
Yingying Fan ◽  
Yang Xu ◽  
...  
Keyword(s):  
Root System ◽  
Candidate Genes ◽  
System Architecture ◽  
Root Traits ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Crown Root ◽  
Genome Wide ◽  
Maize Varieties

Abstract Background: Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear. Methods: In this study, the CRA, CRD, and CRN of 348 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA).Results: A total of 91, 116, and 117 marker–trait associations were identified for CRA, CRD, and CRN, respectively. Additionally, 683 candidate genes within 50 kb of the significant SNPs were identified. A combined analysis of gene annotations and expression profiles revealed 20 promising genes related to auxin synthesis and signal transduction, cytokinin oxidase/dehydrogenase, and transcription factors. These candidate genes may be associated with crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN based on the data for 16SY and 17SY as well as the average values for the three environments. Four haplotypes were detected based on these significant variants, and Hap1 was the optimal haplotype for CRN. Conclusions: These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions.

scholarly journals Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

2019 ◽  
Author(s):  
Marco Giovannetti ◽  
Christian Göschl ◽  
Stig U. Andersen ◽  
Stanislav Kopriva ◽  
Wolfgang Busch
Keyword(s):  
Root System ◽  
System Architecture ◽  
Lotus Japonicus ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Phosphate Limitation ◽  
Plant Responses ◽  
New Genes ◽  
Genome Wide ◽  
Am Symbiosis

AbstractPhosphate is a key nutrient for plants and as it is needed in high quantities. It is highly immobile in the soil and represents a major limiting factor for plant productivity. Plants have evolved different solutions to forage the soil for phosphate and to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as those with arbuscular mycorrhizal fungi (AM symbiosis). Despite the prevalence of AM symbiosis throughout land plants, most studies aimed at identifying genes that regulate plant responses to phosphate have been conducted in species incapable of AM symbiosis, such as Arabidopsis. Here we elucidated plant responses and their genetic basis to different phosphate levels in a plant species that is widely used as a model for AM symbiosis: Lotus japonicus. Rather than focusing on a single model strain, we measured root growth and anion content in response to different levels of phosphate in a large panel of Lotus japonicus natural accessions. This allowed us not only to uncover common as well as divergent responses within this species, but also enabled Genome Wide Association Studies by which we identified new genes regulating phosphate homeostasis in Lotus. Under low phosphate conditions, we uncovered a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. Altogether our data of the genetic and phenotypic variation within a species capable of AM complements studies that have been conducted in Arabidopsis, and advances our understanding of the continuum of genotype by phosphate level interaction that exists throughout dicot plants.Author SummaryPhosphate represents a major limiting factor for plant productivity. Plants have evolved different solutions to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as arbuscular mycorrhizal symbiosis. Here we elucidated plant responses and their genetic basis to different phosphate levels in model legume plant species, Lotus japonicus, a plant commonly used for studying arbuscular mycorhizal symbiosis. We investigated Lotus responses to phosphate levels by combining high throughput root system architecture phenotyping and nutrient measurements with a natural variation approach. We investigated relations between root phenotypic responses and nutrient accumulation and we uncovered, under low phosphate conditions, a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. By means of Genome Wide Association mapping and integration of multiple traits, we identified new genes regulating phosphate homeostasis in Lotus.

scholarly journals Genome-Wide Association Study of Topsoil Root System Architecture in Field-Grown Soybean [Glycine max (L.) Merr.]

2021 ◽  
Vol 11 ◽  
Author(s):  
Arun Prabhu Dhanapal ◽  
Larry M. York ◽  
Kasey A. Hames ◽  
Felix B. Fritschi
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Root System ◽  
System Architecture ◽  
Genome Wide Association Study ◽  
Root Traits ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Unique Snps

Water and nutrient acquisition is a critical function of plant root systems. Root system architecture (RSA) traits are often complex and controlled by many genes. This is the first genome-wide association study reporting genetic loci for RSA traits for field-grown soybean (Glycine max). A collection of 289 soybean genotypes was grown in three environments, root crowns were excavated, and 12 RSA traits assessed. The first two components of a principal component analysis of these 12 traits were used as additional aggregate traits for a total of 14 traits. Marker–trait association for RSA traits were identified using 31,807 single-nucleotide polymorphisms (SNPs) by a genome-wide association analysis. In total, 283 (non-unique) SNPs were significantly associated with one or more of the 14 root traits. Of these, 246 were unique SNPs and 215 SNPs were associated with a single root trait, while 26, four, and one SNPs were associated with two, three, and four root traits, respectively. The 246 SNPs marked 67 loci associated with at least one of the 14 root traits. Seventeen loci on 13 chromosomes were identified by SNPs associated with more than one root trait. Several genes with annotation related to processes that could affect root architecture were identified near these 67 loci. Additional follow-up studies will be needed to confirm the markers and candidate genes identified for RSA traits and to examine the importance of the different root characteristics for soybean productivity under a range of soil and environmental conditions.

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