Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)

We review here our current understanding of the genetic aetiology of the common complex neurological disease multiple sclerosis (MS). The strongest genetic risk factor for MS is the major histocompatibility complex which was identified in the 1970s. In 2011, after a number of genome-wide association studies have been completed and have identified approximately 20 new genes for MS, we ask the question—what is next for the genetics of MS?

Download Full-text

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Frontiers in Plant Science ◽

10.3389/fpls.2020.574674 ◽

2020 ◽

Vol 11 ◽

Author(s):

Paula Arielle Mendes Ribeiro Valdisser ◽

Bárbara S. F. Müller ◽

Janeo Eustáquio de Almeida Filho ◽

Odilon Peixoto Morais Júnior ◽

Cléber Morais Guimarães ◽

...

Keyword(s):

Drought Stress ◽

Common Bean ◽

Genome Wide Association Study ◽

Association Studies ◽

Genetic Material ◽

Genome Wide Association ◽

Abiotic Factor ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Genomic Regions

Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.

Download Full-text

Structure of genetic diversity and genome-wide association studies of bean fly (Ophiomyia spencerella) resistance in common bean

Euphytica ◽

10.1007/s10681-021-02949-y ◽

2021 ◽

Vol 217 (12) ◽

Author(s):

Pascal P. Okwiri Ojwang ◽

Tilly Eldridge ◽

Pilar Corredor-Moreno ◽

Vincent Njung’e

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Association Studies ◽

Sub Saharan Africa ◽

Genome Wide Association ◽

Eastern Africa ◽

Genome Wide Association Studies ◽

Ophiomyia Spencerella ◽

Genome Wide ◽

Bean Fly

AbstractEastern Africa is a significant region of common bean (Phaseolus vulgaris L.) production and genetic diversity. Insect pests are a major biotic constraint in subsistence crop production systems. Bean fly (Ophiomyia spencerella) is a serious pest of beans in eastern Africa highlands. Breeding efforts focus on combining adaptability traits with user preferred seed types. However, lack of information on molecular markers linked to genes modulating bean fly resistance has slowed breeding progress. The objectives were to: (i) characterize genetic diversity and uncover putative bean fly resistant genotypes within diverse seed types and market classes and (ii) identify genomic regions controlling bean fly resistance using genome-wide association analysis (GWAS). A set of 276 diverse genotypes comprising local landraces and varieties from Kenya alongside introductions from International Centre for Tropical Agriculture (CIAT), were assembled. The germplasm represented varied bean production ecologies and seed types. Genetic diversity conforming to Andean and Mesoamerican genepools was established. Out of 276 genotypes evaluated, 150 were Andean, 74 were Mesoamerican and 52 were admixed. Twenty-two genotypes were resistant to bean fly. Association mapping results for stem damage score and plant mortality identified six significant single-nucleotide polymorphisms (SNPs) on chromosomes Pv01 and Pv09. The most significant SNP marker was 12 kilobases downstream of Phvul.001G074900 gene with LOD score > 4.0 hence in linkage disequilibrium with the postulated gene. The identified candidate gene is pleiotropic and modulates both flowering time and plant responses to stress. These findings are a key step towards marker-enabled breeding in common bean for sub-Saharan Africa.

Download Full-text

Genome-Wide Association Studies of Mineral Content in Common Bean

Frontiers in Plant Science ◽

10.3389/fpls.2021.636484 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jerko Gunjača ◽

Klaudija Carović-Stanko ◽

Boris Lazarević ◽

Monika Vidak ◽

Marko Petek ◽

...

Keyword(s):

Common Bean ◽

Mineral Content ◽

Genome Wide Association Study ◽

Association Studies ◽

Manganese Content ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

A Genome ◽

Seed Calcium

Micronutrient malnutrition is one of the main public health problems in many parts of the world. This problem raises the attention of all valuable sources of micronutrients for the human diet, such as common bean (Phaseolus vulgaris L.). In this research, a panel of 174 accessions representing Croatian common bean landraces was phenotyped for seed content of eight nutrients (N, P, K, Ca, Mg, Fe, Zn, and Mn), and genotyped using 6,311 high-quality DArTseq-derived SNP markers. A genome-wide association study (GWAS) was then performed to identify new genetic sources for improving seed mineral content. Twenty-two quantitative trait nucleotides (QTN) associated with seed nitrogen content were discovered on chromosomes Pv01, Pv02, Pv03, Pv05, Pv07, Pv08, and Pv10. Five QTNs were associated with seed phosphorus content, four on chromosome Pv07, and one on Pv08. A single significant QTN was found for seed calcium content on chromosome Pv09 and for seed magnesium content on Pv08. Finally, two QTNs associated with seed zinc content were identified on Pv06 while no QTNs were found to be associated with seed potassium, iron, or manganese content. Our results demonstrate the utility of GWAS for understanding the genetic architecture of seed nutritional traits in common bean and have utility for future enrichment of seed with macro– and micronutrients through genomics-assisted breeding.

Download Full-text

Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean (Phaseolus vulgaris L.)

Frontiers in Plant Science ◽

10.3389/fpls.2019.00962 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 11

Author(s):

Lorenzo Raggi ◽

Leonardo Caproni ◽

Andrea Carboni ◽

Valeria Negri

Keyword(s):

Phaseolus Vulgaris ◽

Association Study ◽

Common Bean ◽

Flowering Time ◽

Candidate Genes ◽

Time Variation ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Phaseolus Vulgaris L ◽

Genome Wide

Download Full-text

Genome-Wide Association Study of Resistance to Bean Fly and Population Structure of Market Classes of Common Bean

10.1101/633545 ◽

2019 ◽

Author(s):

Pascal P. Okwiri Ojwang ◽

Tilly Eldridge ◽

Pilar Corredor-Moreno ◽

Vincent Njung'e

Keyword(s):

Population Structure ◽

Common Bean ◽

Southern Africa ◽

Gene Pool ◽

Association Studies ◽

Genome Wide Association ◽

Chromosome 1 ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Bean Fly

Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southern Africa region is widely driven by choice of grain types, which is affecting the genetic composition and adaptation to target production environments for biotic and abiotic constraints. Two bean fly species, Ophiomyia spencerella and Ophiomyia phaseoli are harmful insect pests of beans causing significant yield losses. Our objectives were to assess the population structure of common bean germplasm of different market classes and to identify polymorphic loci associated with resistance to O. spencerella. The study was carried out on a diversity panel of 284 genotypes using 9040 SNP markers. The genotypes were differentiated in to 14 distinct clusters. The mean FST of 0.4849, revealed major differentiation among the populations. Andean gene pool was more diverse compared to Mesoamerica gene pool which could be attributed to preference for large seeded cultivars. Multi-dimensional scaling and structure analyses revealed admixture among seed types. From genome wide association studies (GWAS), major genomic regions associated with O. spencerella resistance were identified on chromosome 1 (Pv01). The most significant SNP on Pv01 was aligned to gene PHAVU_001G075500g that is related to the Interleukin-1 receptor-associated kinase (IRAK) pathway, critical in regulating inherent immune responses to disease infection and insect herbivore attack. The diversity uncovered on the basis of market classes of beans and the presence of QTL regions associated with resistance to bean fly could serve as a valuable genetic resource for improvement of beans of different seed types in eastern and southern Africa region.

Download Full-text

Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean

Genes ◽

10.3390/genes12050765 ◽

2021 ◽

Vol 12 (5) ◽

pp. 765

Author(s):

Jean Fausto de Carvalho de Carvalho Paulino ◽

Caléo Panhoca de de Almeida ◽

César Júnior Bueno ◽

Qijian Song ◽

Roberto Fritsche-Neto ◽

...

Keyword(s):

Common Bean ◽

Fusarium Wilt ◽

Association Studies ◽

Genome Wide Association ◽

P Value ◽

Genome Wide Association Studies ◽

Progress Curve ◽

Genome Wide ◽

Bonferroni Test ◽

Genomic Regions

Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop’s resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Download Full-text