scholarly journals Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251745
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Caio Cesar Ferrari Barbosa ◽  
Gabriel de Moraes Cunha Gonçalves ◽  
Roberto Fritsche-Neto ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Association Studies ◽  
Colletotrichum Lindemuthianum ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide Association Studies ◽  
Anthracnose Resistance ◽  
Resistant Cultivars ◽  
Genome Wide ◽  
Selection Of

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.

Selection of representative SNP sets for genome-wide association studies: a metaheuristic approach

2011 ◽  
Vol 6 (6) ◽  
pp. 1207-1218 ◽  
Author(s):  
Gürkan Üstünkar ◽  
Süreyya Özöğür-Akyüz ◽  
Gerhard W. Weber ◽  
Christoph M. Friedrich ◽  
Yeşim Aydın Son
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Selection Of

scholarly journals Genome-wide Association Study-based Identification Genes Influencing Agronomic Traits in Rice (Oryza Sativa L.)

2020 ◽  
Author(s):  
aijun wang ◽  
Xinyue Shu ◽  
yuqi Jiang ◽  
Li Ma ◽  
xiaomei jia ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Candidate Genes ◽  
Human Population ◽  
Agronomic Traits ◽  
Association Studies ◽  
Rice Genome ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide Association Studies ◽  
Genome Wide

Abstract BackgroundRice (Oryza sativa L.) is one of the most important cereal crops, providing the daily dietary intake for approximately 50% of the global human population. To needs of the rapidly increasing human population worldwide, cultivation of rice varieties with high yield and quality, more genes or QTLs association with yield traits are required.ResultsCurrently, correlations among different traits and gene interactions both affect the rice breeding. Here, we re-sequenced 259 rice accessions, generating 1, 371.65 Gb of raw data. Furthermore, we performed genome-wide association studies (GWAS) on 13 agronomic traits using 2.8 million single nucleotide polymorphisms (SNPs) characterized in 259 rice accessions. Phenotypic data and best linear unbiased prediction (BLUP) values of each of the 13 traits over two years of each trait were used for GWAS. The result showed that 816 SNP signals were significantly associated (−log10P≥5) with the 13 agronomic traits. We detected candidate genes related to target traits within 200 kb upstream and downstream of the associated SNP loci, based on linkage disequilibrium (LD) blocks in the whole rice genome. These candidate genes were further identified though haplotype block construction. ConclusionsThis study provides an important genomic resource and valuable new information for breeding high yielding breeding rice cultivars through genomic selection.

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