Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean

Abstract

Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co–4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co–4 is localized. Three SCAR markers with known linkage to Co–4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK–4 loci found in previous studies. It is possible that the Co–4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

“…The kinases at the Co-4 locus have been reported to provide PTI in common bean [28]. Burt et al [27] hypothesized that the presence of unique genes in addition to LRR and kinase proteins at the Co-4 gene cluster may be imparting resistance. The hypothesis seems to be correct as the transcriptomic data from present investigation revealed two unannotated genes.…”

“…These kinases belong to receptor like kinase family [25, 27, 28, 95]. Receptor kinases play significant role in the recognition, signal transduction that ultimately lead to disease resistance [25, 27, 28, 96, 97, 98, 99]. The majority of cloned plant disease resistance genes encode proteins such as NBS, LRR, STK that are responsible for perception of avirulence proteins either directly or indirectly.…”

“…Anthracnose resistance is dominant at all loci except the Co-8 locus, and multiple alleles have been identified at the Co-1 , Co-3 , Co-4 , and Co-5 loci. Fine mapping of some of these resistance genes, Co-x [25]; Co-1 [23]; Co-1 2 [26] and the Co-4 2 [27, 28] has been conducted and candidate genes associated with resistance identified. The Co-x gene was fine mapped to Pv01, adjacent to the Co-1 locus [25] and fine mapping of the Co-4 ( COK-4 ) locus revealed 18 copies of the COK-4 gene in a 325 kb segment of Pv08 [28].…”

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

“…Systematic studies on identification and mapping of anthracnose resistance genes in the United States, Canada, Brazil, and France resulted in the identification of around 25 anthracnose resistance genes. Most of the anthracnose resistance genes are dominant except the co-8 and are mapped to eight bean chromosomes ( Burt et al, 2015 ; Meziadi et al, 2016 ; Zuiderveen et al, 2016 ). Seventeen of these genes are numbered from Co-1 to Co-17 , however many anthracnose resistance genes have alphabets as suffix such as Co-x , Co-y , Co-w , Co-Pa , Co-z , Co-1 HY , and are mapped to bean chromosomes where numbered genes are located ( Zuiderveen et al, 2016 ).…”

Análise da diversidade genética e da expressão de genes candidatos para tolerância ao déficit hídrico no grupo Carioca (Phaseolus vulgaris L.), relacionados ao desenvolvimento do sistema radicular

“…Para conhecer a diversidade genética presente em genótipos de feijão comum, e acessar informações que podem ser usadas em programas de melhoramento para obter genótipos com maior rendimento e adaptados a estresses bióticos e abióticos, estudos usando marcadores moleculares têm sido descritos na literatura (GUPTA, et al, 2008;CORTÊS;BLAIR, 2011;PERSEGUINI et al, 2011;BURT et al, 2015;CICHY et al, 2015;KELLER et al, 2015;DIAZ et al, 2018). Polimorfismos de um único nucleotídeo (SNPs) são marcadores ideais para mapeamento genético e acesso a diversidade devido a abundância e ampla distribuição no genoma (CHAGNE´ et al, 2007 Entre os estresses abióticos, a seca é a que apresenta maior impacto no crescimento e produtividade de feijoeiro (RAO et al, 2014).…”