scholarly journals Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

2021 ◽  
Vol 12 ◽  
Author(s):  
Daniel Ambachew ◽  
Matthew W. Blair
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Aluminum Toxicity ◽  
Root Traits ◽  
Al Toxicity ◽  
Genome Wide Association ◽  
Soil Conditions ◽  
Polygenic Inheritance ◽  
Genome Wide ◽  
Significant Difference

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

scholarly journals Genome-Wide Association Study (GWAS) Reveals The Genetic Basis of Brace Root Angle and Diameter in Maize

2021 ◽  
Author(s):  
Daqiu Sun ◽  
Sibo Chen ◽  
Zhenhai Cui ◽  
Jingwei Lin ◽  
Meiling Liu ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Cells ◽  
Root Angle ◽  
Genome Wide ◽  
Wide Range ◽  
Significant Difference

Abstract Background:Brace roots are an important part of the maize root system. Among brace root traits, brace root angle (BRA) and brace root diameter (BRD) are important components that affect plant growth and development. However, there are no reports on the genetic basis of maize BRA and BRD. Results:Here, a genome-wide association study (GWAS) was conducted using 508 associated populations with extensive natural variation. The broad heritability of BRA and BRD reached 0.91 and 0.82, respectively. The analysis of different subgroups showed that there were significant differences in BRA traits in different subgroups, whereas there was no significant difference in BRD. Evaluation of phenotypic diversity in three different environments showed that BRA and BRD exhibit a wide range of natural variability. In the GWAS, the BRA and BRD were combined with 55,8629 single nucleotide polymorphisms, and four candidate genes were found for BRA within the threshold of P < 1.78×10-6 that were significantly related to BRD). These genes may (1) participate in maize brace root cell wall synthesis through cell transport (GRMZM2G479243); (2) involve hormone signaling pathways in the horizontal expansion of brace root cells (GRMZM2G101928 and GRMZM2G174736); or (3) involve the PLETHORA (PLT1/2) gene (GRMZM2G151934) to promote stem cells and transport expanded cells to affect the growth of root meristems.Conclusions:These results provide theoretical information for understanding the genetic basis of brace root development. Further research on candidate genes will help clarify the molecular pathways regulating BRA and BRD in maize.

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.

Genome‐wide association analysis of resistance to aluminum toxicity in the roots of common bean seedlings

Crop Science ◽  
2021 ◽  
Author(s):  
Farai Siamasonta ◽  
Justine Njobvu ◽  
Swivia M. Hamabwe ◽  
Kalaluka Munyinda ◽  
Kelvin Kamfwa
Keyword(s):  
Common Bean ◽  
Association Analysis ◽  
Aluminum Toxicity ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

2021 ◽  
Author(s):  
Lei Wu ◽  
Yujie Chang ◽  
Lanfen Wang ◽  
Shumin Wang ◽  
Jing Wu
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Drought Resistance ◽  
Survival Rates ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Chromosome 11 ◽  
Genome Wide ◽  
A Genome

Abstract A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3832340 SNPs. The coefficient of variation ranged from 40.90% to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

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 Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Peng Zhang ◽  
Kaizhen Zhong ◽  
Zhengzheng Zhong ◽  
Hanhua Tong
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
High Rate ◽  
Genome Wide Association ◽  
Genetic Mechanism ◽  
Al Tolerance ◽  
Genome Wide ◽  
Significant Difference

Abstract Background The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice. Results Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting’s core collection constructed from 2262 Ting’s collections with more than 3.8 million SNPs. Within Ting’s core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance. Conclusions The present study provided important information for further using these elite genes existing in Ting’s core collection for improvement of rice Al tolerance.

scholarly journals Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean

2021 ◽  
Vol 12 ◽  
Author(s):  
Alvaro Soler-Garzón ◽  
Phillip E. McClean ◽  
Phillip N. Miklas
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Genome Wide Association ◽  
Bzip Transcription Factor ◽  
Necrosis Virus ◽  
Host Group ◽  
Host Pathogen Interaction ◽  
Genome Wide ◽  
A Genome ◽  
Host Pathogen

Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-ud to reflect this change; (v) bc-ud alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-ud is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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