Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping—A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)

Abstract

Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7–36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8–27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91–23.36 and Pv11:52.4. A lipoxgenase-1 ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.

Modified screening method of middle american dry bean genotypes reveals new genomic regions on Pv10 associated with anthracnose resistance

“…The mhtplot() function in the R package gap was used to generate the final Manhattan plot ( R Core Team, 2013 ; ). Highly significant markers were defined as those falling outside the 0.01 percentile tail of the empirical distribution of p-values after 10,000 bootstraps ( Mamidi et al., 2014 ; Moghaddam et al., 2016 ; Oladzad et al., 2019a ; Oladzad et al., 2019b ; Oladzad et al., 2020 ; Simons et al., 2021 ) and drawn as horizontal bars on the Manhattan plots. The phenotypic contribution of the markers was evaluated, using likelihood ratio R2 analyses of peak SNP markers with low p-values using the R package, genABEL ( Sun et al., 2010 ).…”

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

“…Although the study of CBB resistance has been ongoing in several common bean and tepary bean genotypes for many years, no CBB resistance gene has been identified. To date, at least 30 quantitative trait loci (QTLs) for CBB resistance have been mapped, and these are primarily located on chromosomes 2, 3, 6, 7, 8, and 11 ( Jung et al, 1996 ; Miklas et al, 2003 ; Liu et al, 2008 ; Shi et al, 2011 ; Viteri et al, 2014 ; Singh and Miklas, 2015 ; Xie et al, 2017 ; Simons et al, 2021 ). However, only three QTLs associated with the linked molecular markers BC420 on chromosome Pv06, SU91 on Pv08 and SAP6 on Pv10 were considered to have major effects and were used for marker-assisted selection (MAS; Fourie et al, 2011 ).…”

Association mapping for common bacterial blight in carioca beans

“…Common bean accounts for a considerable proportion of daily nutrients (Assefa et al 2019). Yield losses caused by plant diseases may reach up to 100%, depending on the aggressiveness of the pathogen (Simons et al 2021). Xap is a gram-negative group of γ-proteobacteria.…”

“…Using chemical control as the main treatment is not effective as the pathogen is quite diverse (Rava and Sartorato 1994). CBB genetic architecture involves both minor and major genes (Simons et al 2021). Until now, up to 25 minor effect resistance loci have been identified across the common bean genome (Simons et al 2021).…”

“…CBB genetic architecture involves both minor and major genes (Simons et al 2021). Until now, up to 25 minor effect resistance loci have been identified across the common bean genome (Simons et al 2021).…”