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Common bean (Phaseolus vulgaris L.) is an important crop in many countries (Uebersax et al., 2022). It is a major source of protein, fiber, carbohydrates and micro nutrients (iron and zinc) (Broughton et al., 2003;Buruchara et al., 2011). Common bean is genetically diverse and is classified into several market classes mainly based on seed characteristics. Yellow beans are a major market class of common bean particularly in Africa (Sichilima et al., 2016). Yellow beans have become popular with consumers due to their faster cooking time and nutritional superiority to other market classes (Sichilima et al., 2016;Wiesinger et al., 2018). They not only contain high levels of iron, a nutrient that is deficient in most African diets, but most of this iron has high bioavailability (Wiesinger et al., 2016;Sadohara et al., 2022). Despite their nutritional superiority, the productivity of yellow beans remains low.Anthracnose (ANT) caused by the fungus Colletotrichum lindemuthianum is a major contributor to this low productivity of the yellow beans. It can cause yield losses of up to 100% in highly susceptible genotypes and when environmental conditions favor its spread (Singh and Schwartz, 2010). ANT is a seedborne disease that can be controlled effectively with the use of fungicides (Mohammed 2013). However, chemical control is not affordable for the majority of smallholder farmers. Development and use of resistant varieties is the most cost-effective control strategy for ANT (Singh and Schwartz, 2010). Although ANT resistance is present in many other market classes, transferring this resistance into the yellow bean background remains challenging due to the poor recovery of the yellow seed coat (particularly the Manteca type) when yellow beans are crossed with other market classes. Therefore, identifying sources of resistance within the yellow market class and elucidating the genetic basis of that resistance could play a critical role in improving ANT resistance in yellow beans Extensive variability in C. lindemuthianum exists at several levels including within field, across production regions within a country, and at both regional and global scales. A recent study aimed at understanding the race structure of C. lindemuthianum in Zambia reported 50 races within the country (Sansala et al., 2024). Globally, more than 300 races have been reported (Nunes et al., 2021;Sansala et al., 2024). Previous studies on race characterization have revealed an intra-race diversity, suggesting that virulence diversity is greater than what is captured by classifications based solely on differential cultivars (Sansala et al., 2024;Mahuku et al., 2004). These races are generally classified as either Andean or Middle American based on the gene pool of the host genotype from which they were isolated. Typically, Andean races are isolated from Andean genotypes and are highly virulent on Andeans. Middle American races are isolated from Middle American genotypes and highly virulent on Middle American genotypes though they also attack Andean genotypes and tend to exhibit higher virulence diversity than Andean races. Studies aimed at understanding the genetic variability of C. lindemuthianum in specific production environments as well as identifying sources of resistance are critical for the development of varieties with durable ANT resistance.Resistance to ANT is controlled by mainly major-effect resistance loci named with the prefix 'Co'. To date, 23 major-effect loci have been identified across eight chromosomes (Ferreira et al., 2013;Badiyal et al., 2024). Resistance conferred by these genes follows a gene-for-gene model, and is typically associated with clusters of resistance genes containing NBS-LRR domains. These clusters provide race-specific qualitative resistance (Geffroy et al., 1999;Rodríguez-Suárez et al. 2008;Mungalu et al., 2020;Ferreira et al 2023;Kuwabo et al., 2023;Sinkala et al., 2024). The Co genes have been classified as either Andean or Middle American (Young and Kelly 1996). In addition to these major-effect loci, minor-effect QTL have also been identified. Both major and minor-effect resistance loci provide resistance to specific races of C. lindemuthianum, and there is no single locus that is effective against all races.One effective strategy for developing bean varieties with durable resistance for a specific region is to first characterize the local race structure of C. lindemuthianum, and then conducting genetic studies such as genome-wide association studies (GWAS) or biparental population QTL analyses to identify resistance loci and/or genes for the identified races. This information can then be used to develop a gene pyramid that can confer effective and durable ANT resistance. QTL mapping has widely been used to identify genomic regions conferring ANT resistance. Some of the identified QTL have co-localized with known Co major ANT resistance loci or previously identified QTL while others are novel (Mungalu et al., 2020;Kachapulula et al., 2025). The QTL analyses results involving multiple races have provided better insights into specific genomic regions that provide resistance to specific races of C. lindemuthianum (Mungalu et al., 2020;Kachapulula et al., 2025).The yellow Andean genotypes PI 527538 and Ervilha show significant variation in their responses to different races of C. lindemuthianum under both artificial and natural infection conditions. PI 527538 has a Njano yellow seed coat color while Ervilha has a pale yellow (Manteca) seed coat color which is strongly preferred by consumers in Africa (Sichilima et al., 2016). The genetic basis of the observed variation in ANT resistance between PI 527538 and Ervilha, and their recombinant inbred lines (RILs) remains unknown. The objectives of this study were: (i) characterize four isolates of C. lindemuthianum into races, (ii) identify QTL associated with resistance to these four races, and (iii) identify lines with pyramided resistance to the characterized races.Twelve differential cultivars, four Andean and eight Middle American, were used for race characterization as described by Pastor-Corrales (1991). Table 1 presents the list of these 12 races differential cultivars, their gene pool, resistance genes, binary numbers and numeric value used to assign race numbers based on their susceptibility to a specific isolate (Young and Kelly 1996).This study used a total of 220 F5:9 RILs derived from a cross between the Andean genotypes PI 527538 and Ervilha to identify QTL conferring resistance to C. lindemuthianum races.However, the number of RILs evaluated varied from 132 (Race 81) to 220 (Race 6). This variation was caused by differences in germination and also some genotypes not reaching the scoring stage. This population was developed using Single Seed Descent method at Michigan State University (Bassett et al., 2021). PI 527538 was originally collected from Burundi, and has a large seed size (48 g/100 seeds) with a green-yellow color and type I (bush) growth habit (Cichy et al., 2015). Ervilha is an Angolan landrace, with a large seed size (58.2 g/100 seeds) Manteca (pale yellow) seed color and a type I growth habit.Pods that showed typical ANT symptoms such as black lesions with slightly sunken center and dark brown or purplish brown margins (Mohammed 2013) were collected from a bean field at Malashi Research Station (Latitude = -11.80; Longitude = 31.45) in Mpika district of Muchinga province of Zambia, a major bean-growing region. The bean field from where the samples were collected is located at Malashi Research Station, which is a major testing site for disease resistance of the breeding lines from public breeding programs in Zambia. The pods were collected from different Andean breeding lines belonging to the University of Zambia (UNZA) Common Bean Breeding program grown in two consecutive growing seasons. Infected pods were transported to the bean laboratory at UNZA, where fungal isolations were conducted. A previously described protocol (Sansala et al., 2024;Nalupya et al., 2021;Mungalu et al., 2020) was used for fungal isolation and race characterization. Small pieces from the lesion (0.5 to 2 mm) were cut out. These were surface-sterilized (for 2 minutes) using 1% sodium hypochlorite and 70% ethanol, and then rinsed in distilled water.The pieces were then dried at room temperature on paper towel for 30-60 minutes and incubated on petri dishes containing potato dextrose agar (PDA) media (39 g/liter) in the dark for 10 days to allow sporulation. Purified isolates were obtained by streaking diluted spore suspensions from the sporulated plates onto fresh plates. After 24 to 48 hours, a single germinating spore was removed from each plate and transferred to a new plate containing fresh PDA to establish single-spore cultures. The purified cultures were kept in the dark cupboard for 10 days until C. lindemuthianum had sporulated. Distilled water was added to the plates and then the spores dislodged by carefully scraping the top of the mycelia using a glass rod.The scraped off spore suspension water was filtered using a cheese cloth. The filtered spore suspension concentration was measured using the hemacytometer and adjusted to a concentration of 1.2 x 10 6 spores per ml. Tween 20 (0.01%) was then added to the spore suspension (10 μl per 100 ml), which was then ready for simultaneous inoculation of the race differentials, checks, parents and RILs.The race differentials, RILs, parents and checks were planted on Styrofoam trays that had 60 wells (5 cm wide, 5 cm long and 5 cm deep) filled with sterilized soil from the field. Three genotypes (Kabulangeti, Lusaka and G2333) were used as checks. Kabulangeti and Lusaka are Andean Zambian landraces and highly susceptible to ANT. Kabulangeti is purple speckled with type III growth habit while Lusaka is a Manteca yellow variety with type I growth habit.G2333 is Middle American with type III growth habit and is highly resistant to ANT (Young et al., 1998).A completely randomized design with three replications was used. Each replication was comprised of two seeds (two seedlings) of each genotype planted in a well. Therefore, a total of six seedlings per genotype were evaluated across the three replications. The seedlings were inoculated when their dicotyledonous leaves had expanded fully. A handheld sprayer filled with inoculum was used to spray the seedlings canopy, taking care that the underside of the seedlings' leaves was also sprayed. After the spray, seedlings were kept at room temperature for two hours to allow inoculum to dry before they were transferred to the high humidity chamber (95-100% humidity) where they were kept for 72 hours. From the humidity chamber, the trays were transferred to the greenhouse, which was maintained at ambient temperature and humidity with approximately12 hours of natural light to allow for disease development. ANT severity on the seedlings was then scored on a CIAT scale of 1-9 (van Schoohoven and Pastor-Corrales. 1987). A score of 1 was for seedlings with no visible symptoms, 2-3 was for seedlings showing limited necrotic, 4-8 was for seedlings with small to large sporulating lesions, and score of 9 was for severely infected and dead seedlings. The scores of 1-3 were considered as highly resistant, 4-6 as moderately resistant and 7-9 as highly susceptible. For race characterization race differentials with a severity score of 1-3 were considered resistant while a score of 4-9 was considered susceptible (Sansala et al., 2024).Analysis of variance was conducted in R (R Core Team, 2025) software on the severity scores to determine the statistical significance of their differences in their response to the four races.Because the data was not normally distributed, it was first transformed using logarithmic transformation before it was used in ANOVA.Pearson correlation analysis for severity scores among the four races was conducted using a base package in R software to determine relatedness.Broad-sense heritability for each trait was calculated using the variance components, which were computed using the R package lme4 and the following equation:□□ 2 = □□ □□ 2 □□ □□ 2 + □□ □□ 2 □□ ⁄Where H 2 is broad-sense heritability, □□ □□ 2 was variance component for genotype, and □□ □□ 2 was error variance component and r is the number of replications.The population used in this study was previously genotyped and details on how this was conducted can be found in Bassett et al., 2021. Briefly, DNA was harvested from fresh leaves using a DNA extraction kit Macherey-Nagel NucleoSpin Plant II. The DNA was genotyped using the BARCBean12K BeadChip with 12,000 SNPs at the USDA Beltsville AgriculturalResearch Center in Beltsville, MD, USA. A total of 870 SNPs were polymorphic and were used to build eleven linkage groups using the software MapDisto version 2.17 (Lorieux, 2012).The size of linkage map ranged from 25.8 cM (Pv10) to 52.8 cM (Pv02), with a total distance of 439.3 cM for 11 linkage groups. The number of SNPs per linkage group ranged from 24 (Pv05 and Pv11) to 138 (Pv03) (Supplementary Table S1). Composite Interval Mapping in the software R/qtl (Broman et al. 2003) was used to map the QTL for resistance to the four characterized races 6, 7, 81 and 294. To determine the threshold for QTL significance, 1000 permutations were conducted. A LOD score of 3 was used. The software Mapchart was used to plot the linkage maps with QTL on them (Voorrips 2002).Candidate genes were identified using a previously described method (Kuwabo et al., 2023).JBrowse in Phytozome was used to browse the Phaseolus vulgaris v2.1 genome to identify positional candidate genes. A gene was considered as a candidate if it was located within this QTL region (250 kb of the QTL peak) and its product is predicted to function in disease resistance.The four isolates A23-2, A23-1, A23-16 and 22-4-B that were infected on the race differentials were characterized as race 6, 7, 81 and 294, respectively (Table 1). Race 6 is an Andean race that was virulent on Andean differentials MDRK and Perry Marrow. The races 7, 81 and 294were classified as mixed races because they were virulent on both Andean and Middle American differentials as previously described by Zuiderveen et al., 2016 andSansala et al., 2024) (Table 1).Response of the RILs, parents and checks to inoculation with races 6, 7, 81 and 294Significant differences were observed among the RILs in their to the four races. The severity score for the population for race 6 was (Table the 220 RILs that were were highly resistant, were moderately resistant and were susceptible 1). The PI 527538 was highly resistant of while Ervilha was highly susceptible of to race 6 (Table 1). The susceptible checks Kabulangeti and Lusaka had a score of 9 while had a score of of RILs to race 6 a race 7, severity scores ranged from 1-9 with a population of to the RILs that were inoculated with race 7, were highly resistant score of were moderately resistant scores of and 48 were highly susceptible of Ervilha had a severity score of while PI 527538 was susceptible with a score of The checks as as the susceptible checks Kabulangeti and Lusaka were highly susceptible of while the resistant was highly resistant of severity score for race 81 ranged from 1-9 with a population of the 132 RILs that were evaluated for response to this 50 were highly resistant while were highly with in the showing a of the severity scores 1). The PI 527538 was highly resistant score of while Ervilha was susceptible score and the showed that these two were The checks as with the two susceptible checks a score of 9 while the resistant had a score of severity score for the population inoculated with race was the RILs evaluated for their response to this were highly resistant, 48 were moderately resistant and were highly susceptible. The PI 527538 was highly resistant of while Ervilha was moderately resistant of was observed for all four races on both of the severity score The RILs and were the only two that were highly resistant to all four races as in Table correlation in severity score was observed between races 6 and = the correlation was between races 6 and = (Table heritability ranged (Race to (Race 81) with an of total of six on chromosomes and were identified as provided resistance to races 6, 7, 81 and (Table and major QTL was identified at the on provided resistance to both race 6 and The of score for or of for was and for races 6 and was a major QTL that and of resistance in the population to races 6 and race The resistance from the The major of in the large R 2 value is with the observed of the severity which resistance provided by a major total of genes with belonging to a of disease resistance genes (Supplementary Table were identified within the of minor-effect QTL was identified on This QTL of the variation in resistance to race 294. The PI 527538 provided the resistance at this QTL was identified the of This QTL of the variation in resistance to race 6 among the The PI 527538 provided resistance at this were three and that were identified on was located at the of the and was a QTL that of the variation in severity score for race 6 among the which provided resistance to race was also located at the of the and it was also a major QTL with R 2 of The QTL to be identified on was and was a major QTL that of the resistance among the RILs to race 294. The Ervilha the resistant at while the at and A total of resistance genes with and (Supplementary Table were identified within the of this four isolates from Zambia were characterized into four diverse races 6, 7, 81 and studies et al., et al., 2021;Sansala et al., et al., et al., 2023;Sinkala et al., et al., 2025) have reported the of a diverse a number of C. lindemuthianum races in Zambia, this is the first of the of the four races 6, 7, 81 and in Zambia. Race 6 was an Andean race that was virulent on only Andean differentials while the other three races 81 and were mixed as they were virulent on both Andean and Middle American The characterization of Andean races was with the growing of Andean beans in Zambia. The four characterized races are diverse from a small and in two growing which how highly C. lindemuthianum can be in a small This high virulence diversity a to the development of varieties with durable resistance. four identified races in the study have previously been reported in other countries Zambia including the et al., and et al., 2022). Race 81 has previously been reported to be highly in et al., were several genotypes that were highly resistant to the four races used in the However, only two RILs and were highly resistant to all two RILs are important genetic that can be used by the bean breeding on the yellow bean market classes to their resistance. This be the high heritability observed for resistance in this of these two RILs is important as they provide an to the bean when resistance from other market classes because of the poor recovery of the yellow seed coat when with other market and major-effect QTL were identified suggesting that the observed resistance in the population was controlled by both major and of the identified QTL provided resistance to more than two races the race-specific of the resistance provided by these and is with (Mungalu et al., 2020;Ferreira et al., et al., 2023;Sinkala et al., 2024). The race specific resistance of this QTL has been to the of clusters of R genes at these major-effect loci and genes of the resistance to specific large QTL identified in the and provided resistance to races 6 and 81 with the which has previously been from to genomic region et al., 2022). is a Andean locus effective against Andean races and mixed races. of the bean grown in Zambia are Andean and mixed races of C. lindemuthianum are Middle American races have also been reported (Sansala et al., 2024) This that this is a major and resistance locus to race The other two identified QTL in the study not with other previously reported QTL et al., 2024). The of three QTL of which with previously identified QTL the of in ANT particularly in which is different from the qualitative resistance provided by the Co loci et al., 2024). was located in a genomic for disease resistance genes with the A total of resistance genes with and (Supplementary Table were identified within the of and majority of these in and these genes play a major role in race-specific resistance of this QTL on with have previously been reported as candidate genes for ANT resistance QTL et al., QTL was identified on QTL at are major genes for ANT and resistance reported at the of the genes for and and for are also located on of identified in the study is the locus and gene for while at is the Andean locus et al., which that this QTL is different from these Co genes and for Despite a minor-effect it be important in resistance and the qualitative resistance provided by the Co loci, and important in the of the Co loci due to race disease resistance genes with the (Supplementary Table were identified as the candidate gene for resistance to race 6 conferred by the QTL isolates collected from a major bean-growing region of Zambia were characterized as races 6, 7, 81 and 294, This is the first of these races in Zambia. two RILs were highly resistant all four races. A total of six QTL and were identified as conferred resistance to the four characterized races. These QTL of ANT resistance variation among RILs suggesting resistance was controlled by both major and A total of disease resistance genes with and were identified as candidate genes for and at and The two RILs with resistance to all four races a genetic to the bean breeding to the yellow beans for ANT resistance while the QTL analyses have provided information that can be used to develop a strategy for ANT resistance in the yellow bean market and The cooking and iron bioavailability of the Manteca yellow bean (Phaseolus vulgaris and of the genetic resistance to