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

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

Frontiers in Plant Science ◽

10.3389/fpls.2020.590740 ◽

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.

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

BMC Plant Biology ◽

10.1186/s12870-021-03127-x ◽

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.

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

Journal of Experimental Botany ◽

10.1093/jxb/eraa029 ◽

2020 ◽

Vol 71 (8) ◽

pp. 2379-2389 ◽

Cited By ~ 2

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.

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

10.21203/rs.3.rs-136918/v1 ◽

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.

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Genetic dissection of 2-heptenal content in soybean (Glycine max) seed through genome-wide association study

Crop and Pasture Science ◽

10.1071/cp20237 ◽

2020 ◽

Vol 71 (10) ◽

pp. 884

Author(s):

Zhikun Wang ◽

Mingming Yang ◽

Yuanzhuo Wang ◽

Chao Yang ◽

Xue Zhao ◽

...

Keyword(s):

Glycine Max ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Fatty Acid Content ◽

Soybean Seed ◽

Genome Wide Association ◽

Quality Characteristic ◽

Genome Wide ◽

A Genome

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

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