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 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.

Genome-wide association study of physical and microstructure-related traits in peanut shell

2021 ◽  
pp. 1-11
Author(s):  
Kailu Cui ◽  
Feiyan Qi ◽  
Ziqi Sun ◽  
Jingjing Feng ◽  
Bingyan Huang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Potential Contribution ◽  
Peanut Shell ◽  
Nucleotide Polymorphisms ◽  
B Genome ◽  
Genome Wide

Abstract Peanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var. hypogaea, var. vulgaris, var. fastigiata and var. hirsuta was used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var. hypogaea, var. hirsuta, var. vulgaris and var. fastigiata for mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P < 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.

scholarly journals Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 432 ◽  
Author(s):  
Zhang ◽  
Wan ◽  
He ◽  
Lan ◽  
Li
Keyword(s):  
Candidate Genes ◽  
Plant Height ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Plant Density ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Higher Plant ◽  
Genome Wide ◽  
A Genome

Drastic changes in plant height (PH) are observed when maize adapt to a higher plant density. Most importantly, PH is an important factor affecting maize yield. Although the genetic basis of PH has been extensively studied using different populations during the past decades, genetic basis remains unclear in the F1 population, which was a widely used population in production. In this study, a genome-wide association study (GWAS) was conducted using an F1 population consisting of 300 maize hybrids with 17,652 single nucleotide polymorphisms (SNPs) makers to identify candidate genes for controlling PH. A total of nine significant SNPs makers and two candidate genes were identified for PH. The candidate genes, Zm00001d018617 and Zm00001d023659, were the genes most probable to be involved in the development of PH. Our results provide new insights into the genetic basis of PH in maize.

scholarly journals Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1005
Author(s):  
Jie Wang ◽  
Bo Zhu ◽  
Jie Wen ◽  
Qinghe Li ◽  
Guiping Zhao
Keyword(s):  
Association Study ◽  
Pathway Analysis ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Genetic Selection ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Disease control and prevention have been critical factors in the dramatic growth of the poultry industry. Disease resistance in chickens can be improved through genetic selection for immunocompetence. The heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. Our objective was to conduct a genome-wide association study (GWAS) and pathway analysis to identify possible biological mechanisms involved in H/L traits. In this study, GWAS for H/L was performed in 1317 Cobb broilers to identify significant single-nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (p < 1/8068) reached a significant level of association. The significant SNP on GGA 19 (chicken chromosome 19) was in the gene for complement C1q binding protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five identified SNPs (p < 0.05). According to the results of pathway analysis, nine associated pathways (p < 0.05) were identified. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L, and 52 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

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.

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