Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence

Meziadi, Chouaïb; Richard, Manon; Derquennes, Amandine; Thareau, Vincent; Blanchet, Sophie; Gratias, Ariane; Pflieger, Stéphanie; Geffroy, Valérie

doi:10.1016/j.plantsci.2015.09.006

Cited by 121 publications

(106 citation statements)

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“…Through pre-breeding programs, work to identify favorable alleles of genes related to important agronomic traits in wild germplasm and landraces, with subsequent incorporation into improved crops, has been reviewed [17]. The availability of common bean reference genomes [9, 18], in addition to predicted functions for thousands of genes, extends the possibilities for marker-assisted selection, and to increase the efficiency of genetic breeding programs [19]. …”

Section: Introductionmentioning

confidence: 99%

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

et al. 2017

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BackgroundCommon bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.ResultsUsing this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.ConclusionsFor common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3805-4) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

et al. 2017

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“…Another example of large distal R cluster is the multi-resistance I cluster presenting R gene Co-u located at the end of Pv02 containing TNLs sequences. However, some atypical R genes have been observed, including: Co-1 , Co-1 2 , Co-1 3 , Co-1 4 , Co-1 5 , Co-x , and Co-w located at the end of Pv01, and since they are located in a region that does not contain NL sequences [25]. …”

Section: Introductionmentioning

confidence: 99%

Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L.)

Chen

Wang

et al. 2017

PLoS ONE

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Anthracnose is a destructive disease of the common bean (Phaseolus vulgaris L.). The Andean cultivar Hongyundou has been demonstrated to possess strong resistance to anthracnose race 81. To study the genetics of this resistance, the Hongyundou cultivar was crossed with a susceptible genotype Jingdou. Segregation of resistance for race 81 was assessed in the F2 population and F2:3 lines under controlled conditions. Results indicate that Hongyundou carries a single dominant gene for anthracnose resistance. An allele test by crossing Hongyundou with another resistant cultivar revealed that the resistance gene is in the Co-1 locus (therefore named Co-1HY). The physical distance between this locus and the two flanking markers was 46 kb, and this region included four candidate genes, namely, Phvul.001G243500, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. These candidate genes encoded serine/threonine-protein kinases. Expression analysis of the four candidate genes in the resistant and susceptible cultivars under control condition and inoculated treatment revealed that all the four candidate genes are expressed at significantly higher levels in the resistant genotype than in susceptible genotype. Phvul.001G243600 and Phvul.001G243700 are expressed nearly 15-fold and 90-fold higher in the resistant genotype than in the susceptible parent before inoculation, respectively. Four candidate genes will provide useful information for further research into the resistance mechanism of anthracnose in common bean. The closely linked flanking markers identified here may be useful for transferring the resistance allele Co-1HY from Hongyundou to elite anthracnose susceptible common bean lines.

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“…Seventeen independent loci, Co-1 to Co-17 , conditioning resistance have been mapped to eight bean chromosomes (Pv01, Pv02, Pv03, Pv04, Pv07, Pv08, Pv09 and Pv11) [11, 21, 22, 23], and a graphic depiction of the mapped Co genes is displayed in Meziadi et al [24]. 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.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

2016

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Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris–C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.

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Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence

Cited by 121 publications

References 89 publications

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L.)

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

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