QTLs for Orobanche spp. resistance in faba bean: identification and validation across different environments

Broomrapes are holoparasitic plants which infect faba bean (Vicia faba L.), among other legumes. Here, we aimed to identify and validate quantitative trait loci (QTLs) for broomrape resistance in the cross 29H × Vf136 and to investigate the existence of common and specific genomic regions against Orobanche crenata and O. foetida. A genetic map including 171 markers was constructed for QTL analyses. Field trials for O. crenata were conducted during three consecutive seasons at Córdoba (Spain) and in a single season at Kafr El-Sheikh (Egypt). QTL analysis for O. foetida was performed using data from a single season at Beja (Tunisia). Seven QTLs for O. crenata were identified. Oc7 on chromosome VI was detected over 3 years at Córdoba, explaining between 22 and 33 % of the phenotypic variation, which make it the most promising candidate for future marker-assisted breeding for broomrape resistance in faba bean. O. crenata QTLs identified at Kafr El-Sheikh did not co-localize with those identified in Córdoba. Environmental differences together with the diversity of parasitic populations between locations may account for the discrepancy. Three QTLs for O. foetida were detected. Co-localization of Oc8 and Of3 in chromosome V confirms a common resistance against both O. crenata and O. foetida, as previously reported.     

Molecular mapping of soybean aphid resistance genes in PI 567541B

The soybean aphid (Aphis glycines Matsumura) is an important pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. PI 567541B is a newly discovered aphid resistance germplasm with early maturity characteristics. The objectives of this study were to map and validate the aphid resistance genes in PI 567541B using molecular markers. A mapping population of 228 F₃ derived lines was investigated for the aphid resistance in both field and greenhouse trials. Two quantitative trait loci (QTLs) controlling the aphid resistance were found using the composite interval mapping method. These two QTLs were localized on linkage groups (LGs) F and M. PI 567541B conferred resistant alleles at both loci. An additive × additive interaction between these two QTLs was identified using the multiple interval mapping method. These two QTLs combined with their interaction explained most of the phenotypic variation in both field and greenhouse trials. In general, the QTL on LG F had less effect than the one on LG M, especially in the greenhouse trial. These two QTLs were further validated using an independent population. The effects of these two QTLs were also confirmed using 50 advanced breeding lines, which were all derived from PI 567541B and had various genetic backgrounds. Hence, these two QTLs identified and validated in this study could be useful in improving soybean aphid resistance by marker-assisted selection.     

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species.

Abstract

Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F₅ recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.     

Validation of QTLs for Orobanche crenata resistance in faba bean (Vicia faba L.) across environments and generations

Broomrape (Orobanche crenata Forsk.) is a major root–parasite of faba bean (Vicia faba L.), that seriously limits crop cultivation in the whole Mediterranean area. This parasitic weed is difficult to control, difficult to evaluate and the resistance identified so far is of polygenic nature. This study was conducted to identify genetic regions associated with broomrape resistance in recombinant inbred lines (RILs) and to validate their previous location in the original F₂ population derived from the cross between lines Vf6 and Vf136. A progeny consisting of 165 F₆ RILs was evaluated in three environments across two locations in 2003 and 2004. Two hundred seventy seven molecular markers were assigned to 21 linkage groups (9 of them assigned to specific chromosomes) that covered 2,856.7 cM of the V. faba genome. The composite interval mapping on the F₆ map detected more quantitative trait loci (QTL) than in the F₂ analysis. In this sense, four QTLs controlling O. crenata resistance (Oc2–Oc5) were identified in the RI segregant population in three different environments. Only Oc1, previously reported in the F₂ population, was not significant in the advanced lines. Oc2 and Oc3 were found to be associated with O. crenata resistance in at least two of the three environments, while the remaining two, Oc4 and Oc5, were only detected in Córdoba-04 and Mengíbar-04 and seemed to be environment dependent.     

Genetic approaches for breeding heat stress tolerance in faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L.)

Vicia faba L. (faba bean) is an important legume and is cultivated essentially as a cool-season crop. Changes in sowing dates and lack of precipitation expose faba bean crop to drought and heat stresses. The gradual rise in global temperatures owing to climate change is likely to exacerbate the detrimental effects of hot and dry climatic conditions on faba bean cultivation. High temperature stress is particularly damaging to faba bean during the flowering period, when the viability of pollen is critical for successful reproduction. Recent studies have shown that maintenance of protein homeostasis through synthesis of heat shock proteins plays a key role in the heat response of plants. To date, there has been no significant work linking the heat response of faba bean to the repertoire of its heat shock proteins. While quantitative trait loci have been identified for resistance against biotic stresses in faba bean, there is no parallel success with abiotic stresses in this species. Programs aiming at genetic improvement of the heat/drought resistance of this crop by both conventional breeding and molecular breeding methods are hampered because of the large and majorly ill-analyzed genome of faba bean plants. Likewise, molecular and biotechnology-related tools are poorly developed for faba bean; as a result, the fruits of transgenic research developed with model plant species are not reaching this crop. While specifically discussing the prospects for the genetic improvement of faba bean against heat and drought stresses, we highlight the areas of research which need to be strengthened on faba bean.     

Mapping quantitative trait loci controlling common bunt resistance in a doubled haploid population derived from the spring wheat cross RL4452 × AC Domain

Wheat resistance to common bunt is a highly desirable trait for environmentally friendly grain grade protection. Valuable breeding achievements have been made to develop wheat varieties with enhanced resistance to the disease, and mapping of race-specific resistance genes has been reported. However, less is known of the chromosomal regions that control non-race specific resistance to common bunt. In this study, we have characterized a segregating population of 185 doubled haploid spring wheat lines derived from the cross RL4452 × AC Domain. Reactions to a mixture of common bunt races were assessed under field simulated spring-sown conditions in greenhouses in two locations over 2 years. A total 369 polymorphic maker loci including 356 microsatellite loci, five expressed sequences tag (ESTs), and eight genes were used to develop a linkage map. Quantitative trait loci (QTL) analysis using composite interval mapping detected three QTLs associated with common bunt resistance, of which two were located on chromosome 1B and one on chromosome 7A. AC Domain alleles contributed the common bunt resistance at all three QTLs. Usefulness of gene tagging within the identified chromosomal regions for common bunt resistance breeding is discussed.     

Exploring the quantitative resistance to <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> pv. <Emphasis Type="Italic">phaseolicola</Emphasis> in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Pseudomonas syringae pv. phaseolicola is an important disease that causes halo blight in common bean. The genetic mechanisms underlying quantitative halo blight resistance are poorly understood in this species, as most disease studies have focused on qualitative resistance. The present work examines the genetic basis of quantitative resistance to the nine halo blight races in different organs (primary and trifoliate leaf, stem and pod) of an Andean recombinant inbred line (RIL) progeny. Using a multi-environment quantitative trait locus (QTL) mapping approach, 76 and 101 main-effect and epistatic QTLs were identified, respectively. Most of the epistatic interactions detected were due to loci without detectable QTL additive main effects. Main and epistatic QTLs detected were mainly consistent across the environment conditions. The homologous genomic regions corresponding to 26 of the 76 main-effect detected QTLs were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins and known defence genes. Main-effect QTLs for resistance to races 3, 4 and 5 in leaf, stem and pod were located on chromosome 2 within a 3.01-Mb region, where a cluster of nine NL genes was detected. The NL gene Phvul.002G323300 is located in this region, which can be considered an important putative candidate gene for the non-organ-specific QTL identified here. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for halo blight resistance in common bean.     

Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean (Phaseolus vulgaris L.)

The objective of this research was to determine the quantitative trait loci (QTLs) controlling phenological traits (days to flowering, days to end of flowering, days to harvest as green pod, and days to maturity), seed size traits (seed length, seed height, seed width, and seed weight), and seed quality traits (water absorption, and coat proportion), in common bean. A population of 104 F₇ recombinant inbred lines (RILs) derived from an inter-gene pool cross between Xana, and Cornell 49242, was used to develop a genetic linkage map including 175 AFLPs, 27 microsatellites, 30 SCARs, 33 ISSRs, 12 RAPDs, 13 loci codifying for seed proteins, and the four genes Fin,fin (growth habit); Asp,asp (seed coat shininess); P,p (seed color); and I,i (resistance to bean common mosaic virus). The map has a total length of 1,042 cM distributed across 11 linkage groups aligned to those of the core linkage map of bean using common molecular markers as anchor points. The QTL analyses were carried out over three environments using the mean environment data with composite interval mapping. Thirty-one QTLs for ten traits were found to be significant in at least one environment and in the mean environment data, the number of significant QTLs identified per trait ranging from two to five. Twenty-seven of these QTLs mapped forming clusters in eight different chromosomal regions. The rationale for this clustered mapping and the possible relationship between some QTLs for phenological traits and the genes Fin and I are discussed.     

Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L.) under different environments

ABSTRACT: BACKGROUND: Common bean (Phaseolus vulgaris L.) is the most important grain legume for human diet worldwide and the angular leaf spot (ALS) is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL) controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse. RESULTS: QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%). This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4%) under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance. CONCLUSIONS: The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b marker is a potential tool for marker assisted selection for ALS resistance.     

Multi-environment mapping and meta-analysis of 100-seed weight in soybean

100-Seed weight (100-SW) of soybean is an important but complicated quantitative trait to yield. This study was focus on the quantitative trait loci (QTLs) of soybean 100-SW from 2006 to 2010, using recombination inbred lines population that was derived from a cross between Charleston and Dongnong 594. A total of 23 QTLs for 100-SW were detected in the linkage group C2, D1a, F, G and O. Nine QTLs were identified by composite interval mapping including one QTL with the minimum confidence interval (CI) of 1.3?cM, while 14 QTLs by multiple interval mapping. Furthermore, 94 reported QTLs of 100-SW were integrated with our QTL mapping results using BioMercator. As a result, 15 consensus QTLs and their corresponding markers were identified. The minimum CI was reduced to 1.52?cM by the combination of meta-analysis. These findings may merit fine-mapping of these QTL in soybean.     

Anchoring of genetic linkage maps to the chromosome complement of Vicia faba L.

Using amplification of marker sequences with DNA from a set of distinct microdissected Vicia faba L. chromosomes covering the entire genome, we could unambiguously show that the linkage group I.B, which includes the pseudogene of legumin B4 (ψ1) and was previously ascribed to the metacentric chromosome I, actually belongs to chromosome IV. By considering the breakpoints of the translocated BKH chromosomes III and IV, even the subchromosomal position of loci LG085 and CNGC4 could be inferred. Anchoring all linkage groups to distinct faba bean chromosomes will facilitate quantitative trait locus fine mapping and gene identification using synteny, and will boost the development of efficient markers for selection in breeding programs.     

Toward an Integrated Linkage Map of Common Bean. III. Mapping Genetic Factors Controlling Host-Bacteria Interactions

Restriction fragment length polymorphism (RFLP)-based genetic linkage maps allow us to dissect the genetic control of quantitative traits (QT) by locating individual quantitative trait loci (QTLs) on the linkage map and determining their type of gene action and the magnitude of their contribution to the phenotype of the QT. We have performed such an analysis for two traits in common bean, involving interactions between the plant host and bacteria, namely Rhizobium nodule number (NN) and resistance to common bacterial blight (CBB) caused by Xanthomonas campestris pv. phaseoli. Analyses were conducted in the progeny of a cross between BAT93 (fewer nodules; moderately resistant to CBB) and Jalo EEP558 (more nodules; susceptible to CBB). An RFLP-based linkage map for common bean based on 152 markers had previously been derived in the F(2) of this cross. Seventy F(2)-derived F(3) families were inoculated in separate greenhouse experiments with Rhizobium tropici strain UMR1899 or X. c. pv. phaseoli isolate isolate W18. Regression and interval mapping analyses were used to identify genomic regions involved in the genetic control of these traits. These two methods identified the same genomic regions for each trait, with a few exceptions. For each trait, at least four putative QTLs were identified, which accounted for approximately 50% and 75% of the phenotypic variation in NN and CBB resistance, respectively. A chromosome region on linkage group D7 carried factor(s) influencing both traits. In all other cases, the putative QTLs affecting NN and CBB were located in different linkage groups or in the same linkage group, but far apart (more than 50 cM). Both BAT93 and Jalo EEP558 contributed alleles associated with higher NN, whereas CBB resistance was always associated with BAT93 alleles. Further investigations are needed to determine whether the QTLs for NN and CBB on linkage group D7 represent linked genes or the same gene with pleiotropic effects. Identification of the QTLs raises the possibility of initiating map-based cloning and marker-assisted selection for these traits.     

鲤饲料转化率性状的QTL 定位及遗传效应分析

数量性状(QTL)定位是实现分子标记辅助育种、基因选择和定位、培育新品种及加快性状遗传研究进展的重要手段。饲料转化率是鲤鱼的重要经济性状和遗传改良的主要目标, 而通过QTL 定位获得与饲料转化率性状紧密连锁的分子标记以及相关基因是遗传育种的重要工具。研究利用SNP、SSR、EST-SSR 等分子标记构建鲤鱼(Cyprinus carpio L.)遗传连锁图谱并对重要经济性状进行QTL 定位。选用174 个SSR 标记、41 个EST-SSR 标记、345 个SNP 标记对德国镜鲤F2 代群体68 个个体进行基因型检测, 用JoinMap4.0 软件包构建鲤鱼遗传连锁图谱。再用MapQTL5.0 的区间作图法(Interval mapping, IM)和多QTL 区间定位法(MQMMapping, MQM)对饲料转化率性状进行QTL 区间检测, 通过置换实验(1000 次重复)确定连锁群显著性水平阈值。结果显示, 在对饲料转化率性状的多QTL 区间定位中, 共检测到15 个QTLs 区间, 分布在9 个连锁群上, 解释表型变异范围为17.70%—52.20%, 解释表型变异最大的QTLs 区间在第48 连锁群上, 为52.20%。HLJE314-SNP0919(LG25)区间标记覆盖的图距最小, 为0.164 cM; 最大的是HLJ1439-HLJ1438(LG39)区间,覆盖图距为24.922 cM。其中区间HLJ1439-HLJ1438、HLJ922 -SNP0711 解释表型变异均超过50.00%, 可能是影响饲料转化率性状的主效QTLs 区间。与饲料转化率相关的15 个QTLs 的加性效应方向并不一致, 有3个区间具有负向加性效应, 平均为?0.027; 12 个正向加性效应, 平均值为0.06。研究检测出的与鲤鱼饲料转化率性状相关的QTL 位点可为鲤鱼分子标记辅助育种和更进一步的QTL 精细定位打下基础。       

Genetic resolution and verification of quantitative trait loci for flowering and plant height with recombinant inbred lines of maize.

Recombinant inbred (RI) lines offer several advantages for detecting quantitative trait loci (QTLs), including increased precision of trait measurements, power for detection of additive effects, and resolution of linked QTLs. This study was conducted to detect and characterize QTLs in maize for flowering and plant height and to compare QTL detection in an early (F2:3) generation of the same population. One hundred and eighty-six RIs from a cross between inbred lines Mo17 and H99 were evaluated in a replicated field experiment and analyzed at 101 loci detected by restriction fragment length polymorphisms. QTLs were identified by single-factor analysis of variance. A total of 59 QTLs were detected for plant height, ear height, top height, anthesis, silk emergence, and anthesis to silk interval. Individual QTLs explained 2.2-15.4% of trait variation, and multiple models including all QTLs detected for a trait explained up to 52.5% of the phenotypic variation. Comparison of QTLs detected with 150 F2:3 lines from the same population indicated that 16 (70%) of the 23 F2:3 QTLs were also observed in the F6:7 generation. Parental effects were consistent across generations. At 14 of the 16 QTLs detected in both generations, genetic effects were smaller in the F6:7. Also, some QTLs detected in the F2:3 were resolved into multiple linked QTLs in the F6:7, indicating the additional power of RI populations for mapping, with important implications for marker-assisted selection as well as map-based cloning of QTLs. Key words : Zea mays, RFLP, plant breeding, genetics, recombination.     

Generation and characterization of 11 novel est derived microsatellites from Vicia faba (Fabaceae)

? Premise of the study: Simple sequence repeat (SSR) markers were developed for faba bean using expressed sequence tags (ESTs) from the NCBI database to study for genetic diversity. ? Methods and Results: A total of 11 novel EST-SSR loci were generated and characterized when tested on four populations of 29 faba bean individuals from China and Europe. The number of alleles (A) ranged from 1 to 3 in each population, and observed heterozygosity (H(O)) and expected heterozygosity (H(E)) ranged from 0 to 0.5000 and 0.6400, respectively. Furthermore, transferable analysis revealed that eight of these loci (72.73%) amplified in Pisum sativum L., six of which (75.00%) detected polymorphism. ? Conclusions: The developed markers in this study will provide valuable tools for genetic diversity, resource conservation, genetic mapping, and marker-assisted breeding of faba bean in the future.     

QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium

Asiatic cotton(Gossypium arboreum L.) is an Old World cultivated cotton species.The sinense race was planted extensively in China.Due to the advances in spinning technology during the last century,the species was replaced by the New World allotetraploid cotton G.hirsutum L.Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs.In addition,G.arboreum serves as a model for genomic research in Gossypium.In the present study,we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 1 3 linkage groups.The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci.A population containing 1 76 F2:3 families was used to perform quantitative trait loci(QTL)mapping for 17 phenotypes using Multiple QTL Model(MQM)of MapQTL ver 5.0.Overall,108 QTLs were detected on 13 chromosomes.Thirty-one QTLs for yield and its components were detected in the F2 population.Forty-one QTLs for yield and its components were detected in the F2:3 families with a total of 43 QTLs for fiber qualities.Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2:3.Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals.These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.     

Mapping QTLs for sucrose content,yield and quality in a sugar beet population fingerprinted by EST-related markers

Seventy five expressed sequence tags (ESTs) that are associated with functions in carbohydrate and nitrogen metabolism were genotyped in 108 plants of an F2 population of sugar beet ( Beta vulgaris L.) segregating for sugar quality and yield parameters. Supplemented by known RFLP and AFLP markers, the resulting map spans 446 cM of the 758-Mbp genome of sugar beet. F3 test-cross plants were analysed for corrected sugar yield, beet yield, ion balance and the content of sugar, amino nitrogen, potassium and sodium in six locations. Twenty one significant quantitative trait loci (QTLs) were detected using the composite interval mapping approach. Expressed genes flanking the QTLs were identified in all cases. Correlations between QTLs and potential candidate genes are discussed.     

Mapping of quantitative trait loci for a new source of resistance to bruchids in the wild species Vigna nepalensis Tateishi & Maxted (Vigna subgenus Ceratotropis)

Azuki bean breeders have long been interested in producing azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi] varieties with bruchid resistance. A new bruchid (Callosobruchus spp.) resistance source was found in V. nepalensis Tateishi & Maxted, a species that is cross compatible with azuki bean. Quantitative trait loci (QTLs) analysis for resistance to C. chinensis (L.) and C. maculatus (F.) was conducted using F(2) (V. nepalensis x V. angularis) and BC(1)F(1) [(V. nepalensis x V. angularis) x V. angularis] populations derived from crosses between the bruchid resistant species V. nepalensis and bruchid susceptible species V. angularis. Resistance was measured using two traits, percentage of seeds damaged by bruchids and the time taken for adult bruchids to emerge from seeds. Based on the results from both populations seven QTLs were detected for bruchid resistance; five QTLs for resistance to C. chinensis and two QTLs for resistance to C. maculatus. The different locations found for some resistance QTL to the two bruchid species suggests different resistance mechanisms. QTLs on linkage group (LG) 1 and LG2 for bruchid resistance to C. chinensis co-localized with seed size QTLs suggesting that incremental increase in seed size accompanied susceptibility to C. chinensis. Based on linked markers the QTL on these two linkage groups appear to be the same as previously reported in other Asian Vigna. However, several other QTLs were newly detected including one on LG4 that appears unrelated to seed size. Transfer of these new sources of bruchid resistance from V. nepalensis to azuki bean will be aided by the progress being made in azuki genome mapping.     

Genetic variation underlying pod size and color traits of common bean depends on quantitative trait loci with epistatic effects

Common bean is an important vegetable legume in many regions of the world. Size and color of fresh pods are the key factors for deciding the commercial acceptance of bean as a fresh vegetable. The genetic basis of important horticultural traits of common bean is still poorly understood, which hinders DNA marker-assisted breeding in this crop. Here we report the identification of single-locus and epistatic quantitative trait loci (QTLs), as well as their environment interaction effects for six pod traits, namely width, thickness, length, size index, beak length and color, using an Andean intra-gene pool recombinant inbred line population from a cross between a cultivated common bean and an exotic nuña bean. The QTL analyses performed detected a total of 23 QTLs (single-locus QTLs and epistatic QTLs): five with only individual additive effects and six with only epistatic effects, while the remaining twelve showed both effects. These QTLs were distributed across linkage groups (LGs) 1, 2, 4, 6, 7, 8, 9, 10 and 11; particularly noteworthy are the QTLs for pod size co-located on LGs 1 and 4, indicative of tight linkage or genes with pleiotropic effects governing these traits. Overall, the results obtained showed that additive and epistatic effects are the major genetic basis of pod size and color traits. The mapping of QTLs including epistatic loci for the six pod traits evaluated provides support for implementing marker-assisted selection toward genetic improvement of common bean.