scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
Snp Marker ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

2019 ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Stem Canker ◽  
Snp Marker ◽  
P Value ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association ( p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R² = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression

scholarly journals Association mapping of a locus that confers Southern stem canker resistance in soybean

2019 ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
P Value ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous) is an important soybean disease, which has been responsible for severe losses in the past. The main strategy to control this fungus is through the introgression of resistance genes. So far, five main loci have been associated with resistance to Southern stem canker. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers useful in breeding programs. Results We characterized the response to Southern stem canker infection in a panel of 295 accessions from different regions of the world including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped and we identified marker loci associated with Diaporthe aspalathi resistance using GWAS analysis. We identified 19 SNPs associated with Southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a high level of the phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi present inn most of the lines comprising this panel. We also identified in resequenced soybean materials other SNPs in the region identified by GWAS in the same LD block that clearly differentiate resistance and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% of selection efficiency. Conclusions Our results suggest a relevant importance of this locus in SSC resistance in soybean cultivars and accessions from different countries and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select resistance materials against this pathogen and support its introgression.

scholarly journals Identification and fine-mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and production markers validation in breeding lines

2021 ◽  
Author(s):  
Jiaojiao Ren ◽  
Penghao Wu ◽  
Gordon M. Huestis ◽  
Ao Zhang ◽  
Jingtao Qu ◽  
...  
Keyword(s):  
Latin American ◽  
Fine Mapping ◽  
Genome Wide Association Study ◽  
Selective Genotyping ◽  
Doubled Haploid Population ◽  
Phenotypic Variance ◽  
Breeding Lines ◽  
A Genome ◽  
Tar Spot ◽  
Major Qtl

Abstract Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively. A total of 115 SNPs in bin 8.03 were detected by GWAS and three QTL in bins 6.05, 6.07, and 8.03 were detected by selective genotyping. The major QTL qRtsc8-1 located in bin 8.03 was detected by both analyses, it explained 14.97% of the phenotypic variance. To fine-map qRtsc8-1, the recombinant-derived progeny test was implemented. Recombinations in each generation were backcrossed, and the backcross progenies were genotyped with Kompetitive Allele Specific PCR (KASP) markers and phenotyped for TSC resistance individually. The significant tests for comparing the TSC resistance between the two classes of progenies with and without resistant alleles were used for fine-mapping. In BC5 generation, qRtsc8-1 was fine mapped in an interval of ~721 kb flanked by markers of KASP81160138 and KASP81881276. In this interval, the candidate genes GRMZM2G063511 and GRMZM2G073884 were identified, which encode an integral membrane protein-like and a leucine-rich repeat receptor-like protein kinase, respectively. Both genes are involved in maize disease resistance responses. Two production markers KASP81160138 and KASP81160155 were verified in 471 breeding lines. This study provides valuable information for cloning the resistance gene, it will also facilitate the routine implementation of marker-assisted selection in the breeding pipeline for improving TSC resistance.

scholarly journals Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel

2021 ◽  
Author(s):  
Alexandra Ficht ◽  
Robert W. Bruce ◽  
Davoud Torkamaneh ◽  
Christopher Grainger ◽  
Milad Eskandari ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genome Wide Association Study ◽  
Sucrose Concentration ◽  
Soybean Seed ◽  
Breeding Programs ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Important Trait ◽  
Genotype By Sequencing

Abstract Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to understand the genetic variability present for traits of interest in their program germplasm. Sucrose concentration is becoming an increasingly important trait for the production of soy-food products. The objective of this study was to use a genome-wide association study (GWAS) to identify putative QTL for sucrose concentration in soybean seed. A GWAS panel consisting of 266 historic and current soybean accessions was genotyped with 76k genotype-by-sequencing (GBS) SNP data and phenotyped in four field locations in Ontario (Canada) from 2015 to 2017. Seven putative QTL were identified on chromosomes 1, 6, 8, 9, 10, 13 and 14. A key gene related to sucrose synthase (Glyma.06g182700) was found to be associated with the QTL found on chromosome 6. This information will facilitate efforts to increase the available genetic variability for sucrose concentration in soybean breeding programs and develop new and improved high-sucrose soybean cultivars suitable for the soy-food industry.

scholarly journals Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1786
Author(s):  
Soumeya Rida ◽  
Oula Maafi ◽  
Ana López-Malvar ◽  
Pedro Revilla ◽  
Meriem Riache ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Seedling Traits ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

scholarly journals Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1220
Author(s):  
Roshan Kulkarni ◽  
Ratan Chopra ◽  
Jennifer Chagoya ◽  
Charles E. Simpson ◽  
Michael R. Baring ◽  
...  
Keyword(s):  
Cost Effective ◽  
Amplicon Sequencing ◽  
Routine Practice ◽  
Specific Information ◽  
Illumina Hiseq ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Cost Effective Approach ◽  
A Genome ◽  
The Cost

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

scholarly journals A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

2020 ◽  
Author(s):  
Rachit K. Saxena ◽  
Anil Hake ◽  
Abhishek Bohra ◽  
Aamir W. Khan ◽  
Anupama Hingane ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Diagnostic Marker ◽  
Development Program ◽  
Cost Effective ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Novel Approach ◽  
Resistant Varieties ◽  
Pathogen Variability

Abstract Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

scholarly journals A genome-wide association study unravels cytokinin as a major component in the root defense responses against Ralstonia solanacearum

2021 ◽  
Author(s):  
Alejandro Alonso-Díaz ◽  
Santosh B Satbhai ◽  
Roger de Pedro-Jové ◽  
Hannah M Berry ◽  
Christian Göschl ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Defense Responses ◽  
Genome Wide Association ◽  
Root Growth Inhibition ◽  
Future Research ◽  
Cytokinin Signaling ◽  
Genome Wide ◽  
A Genome

Abstract Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host’s root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated to the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a Genome-Wide Association Study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role of cytokinin in root immunity, paving the way for future research that will help understanding the mechanisms underpinning root defenses.

scholarly journals Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Şakir Burak Bükücü ◽  
Mehmet Sütyemez ◽  
Sina Kefayati ◽  
Aibibula Paizila ◽  
Abdulqader Jighly ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Genotypic Variation ◽  
Phenotypic Traits ◽  
Juvenile Period ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

scholarly journals Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

2020 ◽  
Vol 21 (12) ◽  
pp. 4263
Author(s):  
Alicja Macko-Podgórni ◽  
Katarzyna Stelmach ◽  
Kornelia Kwolek ◽  
Gabriela Machaj ◽  
Shelby Ellison ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Secondary Growth ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Storage Root ◽  
A Genome ◽  
Elevated Expression ◽  
Edible Roots ◽  
Diverse Groups

Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root.

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