Intra-gene Pool Research Articles

QTL Mapping for Drought-Responsive Agronomic Traits Associated with Physiology, Phenology, and Yield in an Andean Intra-Gene Pool Common Bean Population

Understanding the genetic background of drought tolerance in common bean (Phaseolus vulgaris L.) can aid its resilience improvement. However, drought response studies in large seeded genotypes of Andean origin are insufficient. Here, a novel Andean intra-gene pool genetic linkage map was created for quantitative trait locus (QTL) mapping of drought-responsive traits in a recombinant inbred line population from a cross of two cultivars differing in their response to drought. Single environment and QTL × environment analysis revealed 49 QTLs for physiology, phenology, and yield-associated traits under control and/or drought conditions. Notable QTLs for days to flowering (Df1.1 and Df 1.2) were co-localized with a putative QTL for days to pods (Dp1.1) on linkage group 1, suggesting pleiotropy for genes controlling them. QTLs with stable effects for number of seeds per pod (Sp2.1) in both seasons and putative water potential QTLs (Wp1.1, Wp5.1) were detected. Detected QTLs were validated by projection on common bean consensus linkage map. Drought response-associated QTLs identified in the novel Andean recombinant inbred line (RIL) population confirmed the potential of Andean germplasm in improving drought tolerance in common bean. Yield-associated QTLs Syp1.1, Syp1.2, and Sp2.1 in particular could be useful for marker-assisted selection for higher yield of Andean common beans.

Epistasis in intra- and inter-gene pool crosses of the common bean.

Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses.

An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

The common bean, an important source of protein and minerals for humans, complements cereals both nutritionally and as a rotation crop, supplying nitrogen and reducing soil pathogens. The aim of this study was to develop an operational SNP-based panel for common bean in order to facilitate SSR employment in genetic diversity and population structure analyses, and its use in breeding programs. A set of 88 diverse and important common bean cultivars/lines (53), landraces (33) and wild accessions (2) were genotyped. Overall, the 58 SSRs performed better at evaluating genetic diversity (Ā = 7.38; He = 58.7 %; PI = 1.20E−45) than the 345 SNPs, of which the SSRs dinucleotides (SSR-di) were more informative (Ā = 9.92; He = 72.5 %; PI = 3.40E−26) and a selected set of 13 SSRs (Ā = 15.31/locus; He = 84.5 %; PI = 1.03E−19) allowed for the discrimination of all individuals. For the 345 high-quality scored SNPs a low combined PI (4.70E−119) and high PE (100 %) was obtained for the assessment of parentage and identity. The SNPs were very useful for linkage mapping in inter- (78.2 %) and intra-gene pool (17.7 %) crosses. Both markers afforded high resolution detection of inter-gene pool structure, with greater differentiation based on SNPs (K = 2, F ST = 0.759). The SSRs-di differentiated cultivars/lines and landraces (K = 3) of Mesoamerican origin. A set of 16 SSRs was selected to establish a routine and operational analysis of Genbank accessions allowing an efficient origin-based discrimination of common bean accessions. Operational genotyping panels based on SSRs and SNPs were derived, contributing to the growing integration of genomics with molecular breeding programs of the common bean.

Pyramiding white mould resistance between and within common bean gene pools

Singh, S. P., Schwartz, H. F., Terán, H., Viteri, D. and Otto, K. 2014. Pyramiding white mould resistance between and within common bean gene pools. Can. J. Plant Sci. 94: 947–954. White mould caused by Sclerotinia sclerotiorum (Lib.) de Bary is a severe disease of common bean (Phaseolus vulgaris L.) in North America and similar production regions. Low to high levels of white mould resistance exist in cultivated and wild common bean and the secondary gene pool. But, cultivars with high levels of resistance are not yet available. The objectives of this study were: (1) to combine or pyramid high levels of resistance from multiple-parent populations between and within gene pools, and (2) to compare the response of pyramided breeding lines (PBL) to four isolates of the white mould pathogen with that of known sources of resistance. Two Andean PBL each derived from an Andean intra-gene pool and inter-gene pool, four Middle American pinto bean PBL from one inter-gene pool multiple-parent population, their seven resistant parents, and susceptible pinto, Othello, were inoculated in the greenhouse with pathogen isolates ARS12D and ND710 at University of Idaho, Kimberly in 2012, and isolates CO467 and NY133 at Colorado State University, Fort Collins in 2013. The percentage of resistant plants for the PBL ranged from 62.5 to 81.9, and mean white mould score from 4.0 to 4.6. The respective values for the white mould resistant parents ranged from 3.1 to 57.0 for the percentage of resistant plants and from 4.8 to 7.5 for the mean white mould score. Furthermore, PBL SE154-1 inoculated with isolate ARS12D, and SE152-6 with isolates ARS12D and ND710 had 100% resistant plants. But, only SE153-1 and SE155-9 inoculated with isolates CO467 and NY133 had significantly (P ≤0.05) higher levels of resistance than the most resistant parents A 195 and VA 19. The pinto bean PBL SE153-1, SE153-6, and SE153-7, and Andean types SE152-6 and SE155-9 were the most resistant among all genotypes inoculated with the four isolates of the white mould pathogen in both greenhouses.

Genetic analysis of single-locus and epistatic QTLs for seed traits in an adapted × nuña RIL population of common bean (Phaseolus vulgaris L.)

The QTLs analyses here reported demonstrate the significant role of both individual additive and epistatic effects in the genetic control of seed quality traits in the Andean common bean. Common bean shows considerable variability in seed size and coat color, which are important agronomic traits determining farmer and consumer acceptability. Therefore, strategies must be devised to improve the genetic base of cultivated germplasm with new alleles that would contribute positively to breeding programs. For that purpose, a population of 185 recombinant inbred lines derived from an Andean intra-gene pool cross, involving an adapted common bean (PMB0225 parent) and an exotic nuña bean (PHA1037 parent), was evaluated under six different--short and long-day--environmental conditions for seed dimension, weight, color, and brightness traits, as well as the number of seed per pod. A multi-environment Quantitative Trait Loci (QTL) analysis was carried out and 59 QTLs were mapped on all linkage groups, 18 of which had only individual additive effects, while 27 showed only epistatic effects and 14 had both individual additive and epistatic effects. Multivariate models that included significant QTL explained from 8 to 68 % and 2 to 15 % of the additive and epistatic effects, respectively. Most of these QTLs were consistent over environment, though interactions between QTLs and environments were also detected. Despite this, QTLs with differential effect on long-day and short-day environments were not found. QTLs identified were positioned in cluster, suggesting that either pleiotropic QTLs control several traits or tightly linked QTLs for different traits map together in the same genomic regions. Overall, our results show that digenic epistatic interactions clearly play an important role in the genetic control of seed quality traits in the Andean common bean.

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 nuna 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.

Genetic and phenotypic parameters in common bean segregant populations from intra and inter-gene pool crosses of elite lines

This study aimed compare segregating populations of common bean (Phaseolus vulgaris L.) derived from intra and inter-gene pool crosses of elite lines by estimates of some genetic and phenotypic parameters. Four elite lines highly adapted to Brazilian conditions were used (ESAL 686 and BRS Radiante: Andean gene pool; BRSMG Majestoso and BRS Valente: Mesoamerican gene pool). Two intra-gene pool (“A”: ESAL 686 × BRS Radiante; “B”: BRS Valente × BRSMG Majestoso) and two inter-gene pool segregant populations (“C”: BRS Radiante × BRSMG Majestoso and “D”: ESAL 686 × BRS Valente) were obtained. The parental lines, the cultivar Perola and fifty-five F2:3 progenies of each population were evaluated in the rainy season 2010/2011, and afterwards (F2:4) in dry season of 2011. Estimates of genetic variance (\(\hat{\sigma }_{G}^{2}\)), heritability on a progeny mean basis (\(\hat{h}_{p}^{2}\)), heritability realized (\(\hat{h}_{R}^{2}\)) and gain expected from selection (GS) were obtained at joint analysis, in each population, for the traits number of days to flowering (DTF), 100 seed weight (100SW) and seed yield (SYD). It was observed that for all traits, inter-gene pool crosses (“C” and “D”) showed higher estimates of \(\hat{\sigma }_{G}^{2}\), \(\hat{h}_{p}^{2}\), \(\hat{h}_{R}^{2}\) and GS than intra-gene pool crosses (“A” and “B”), which indicates more genetic variability. However, for SYD, the higher variability was associated to lower average of seed yield, showing that even utilizing adapted parents the inter-gene pool crosses are inferior to crosses between lines of the same gene pool.

Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

Genetics of intra-gene pool and inter-gene pool hybridization for seed traits in common bean ( Phaseolus vulgaris L.) germplasm from Europe

Due to adaptation to new ecological and manmade conditions, the large diversity evolved in the European common bean germplasm is of particular interest for plant breeding. The knowledge of the genetic relationships within and among races and gene pools and their performance per se will provide bean breeders with a starting point in designing crosses using contrasting and complementary parents to broaden the genetic base within the different commercial classes. A genetic study of seed size variation and protein markers in progeny derived from 16 intraracial, interracial and inter-gene pools European common bean populations was conducted. General and specific combining ability (GCA and SCA) values were significant for seed weight, indicating that both additive and nonadditive genetic effects were involved in conditioning seed weight. Interracial populations showed transgressive values due to the accumulation of large-seeded alleles. Genetic variation inside Andean germplasm, and Chile and Peru races in particular, exhibited useful genetic progress in these populations, providing lines with a large seed size, and so, an excellent market potential. The distribution of incompatibility between both gene pools (Mesoamerican and Andean) of the common bean was explored. Inter-gene pool populations provided lower means of inbred segregants than the mid-parent value. Therefore, a good option it would be select for large seed size according to a recurrent or congruity inbred-backcrossing selection programs. Analysis of allele markers frequencies in inter-gene populations showed segregation distortion with a higher than expected frequency of alleles from the Mesoamerican gene pool, many of which were fixed in the F 7 lines. The presence of a great percentage of markers that showed segregation distortion in these populations (87%) indicated that this phenomenon can be amplified by using distance related common bean genotypes. In addition, a high percentage of heterozygotes for the Phs locus (for the seed storage protein phaseolin) was found, which suggest that the Andean homozygous TT could not be expressed in Mesoamerican genetic background due to the action of some form of female specific mechanisms that affected gene exchange between parental germplasm in inter-gene pool populations. The present work provides useful information in the establishment of large seed size germplasm that could have a great deal of interest among breeders and may offer some possibilities to exploit existing variation within and between common bean races.

Plant growth habit, root architecture traits and tolerance to low soil phosphorus in an Andean bean population

The optimal plant growth habit and architecture of common bean (Phaseolus vulgaris L.) is dependent on environmental conditions. The objectives of this research were to determine if plant growth habit impacts a plant’s ability to grow in low P conditions, as measured by P uptake, seed yield, and P use efficiency and to determine if aboveground plant growth habit and root growth are associated at variable P soil levels. The study was carried out with recombinant inbred lines developed from an Andean intra-gene pool cross between a low P tolerant parent with an indeterminate growth habit (G19833) and a low P susceptible parent with a determinate growth habit (AND696). The population was grown for 2 years in low and sufficient P conditions in a field site in Darien, Colombia. In the first season, indeterminate lines had 15% more seed yield than the determinate lines in the low P treatment, whereas there was no difference by growth habit in the high P treatment. In the second season, seed yield and tolerance to low P was not influenced by growth habit. Root architectural characteristics such as root length density (RLD) and root surface area were 25% and 34% greater respectively in the indeterminate lines under P-sufficiency, whereas under low P, root architecture traits were not significantly different by growth habit. Root plasticity was higher in determinate lines, although RLD and root surface area did not play a significant role in tolerance to low P. Overall, the data were consistent with shoot growth habit as playing a complex and important role in adaptation to P-deficiency.

Selection for seed yield in Andean intra-gene pool and Andean × Middle American inter-gene pool populations of common bean

Yields of large-seeded Andean (A) common bean (Phaseolus vulgaris L.) cultivars of Chile and Nueva Granada races are 40 to 60% lower compared to their Middle American (M) counterparts of small-seeded Mesoamerica and medium-seeded Durango races. Our objective was to use the concept of congruity backcrossing between Andean x Middle American inter-gene pool [AM 11833 = A 483 (A)///// A 686 (M) //// PVA 800A(A)/// ‘Carioca’ (M)// Carioca (M)/ G 19833 (A)] and between races within Andean gene pool [i.e., intra-gene pool Andean, AA 11834 = A483 (A)//// ‘Cardinal’(A) /// ‘Blanco Espanol’(A) // BlancoEspanol (A) / ‘Taylor’ (A)] to compare selection for seed yield improvement of large-seeded Andean beans. Seven hundred sixty seven F2-derived F3 (F2:3) families were produced for each population. Visual appraisal for total plant performance, combined with seed yield from non-replicated plots was used for selection of 551 families in F2:3, 182 families in F2:4, and 91 families in F2:5 in each population. Eight hundred twenty three F5:6 lines were developed from the 91 F2:5 families in each population. Visual selection, combined with seed yield in non-replicated plots was again used to select 294 lines in F5:6 in each population. Similarly, 44 highest yielding F5:7 lines were selected in AM 11833 and 39 F5:7 lines in AA 11834. Thus, single plant selections were made in the F2 and F5, and plants within each plot were harvested in bulk in F3, F4, F6, and F7. Thirty nine F5:8 lines from AA 11834 and 44 lines from AM 11833, parents, and checks were evaluated at Popayan and Quilichao, Colombia in 1998 and 1999. Selected lines in both populations, on average, out-yielded the mean of their large-seeded Andean parents. Mean yield of the lines selected from AM 11833 was 50% higher than AA 11834 lines. Twelve F5:8 lines out-yielded the highest yielding Andean parents G 19833 and A 483 in AM 11833, whereas only one line yielded significantly higher (p < 0.05) than the highest yielding parent A 483 in AA 11834. However, none of selected lines out-yielded small-seeded Middle American parents used in AM 11833 (A 686 and ‘Carioca’). The mean 100 seed-weight of AA 11834 was 36 g compared to 28 G for AM 11833 F5:8 lines. Selected lines had similar days to maturity as parents in AM 11833, and matured 3 d later in AA11834. Correlation coefficients between yield and 100 seed-weight were negative in both populations. Yield and days to maturity were positively correlated in AA 11834.

Informatión bioquímica acerca de 1a domesticación de los frijolesPhaseolus

The genusPhaseolus (Fabaceae) consists of some 50 species, all of which are distributed in the Americas. Four of these contain cultigens.P. vulgaris (common bean),P. lunatus (lima bean),P. acutifolius (tepary bean),P. coccineus subsp.coccineus (runner bean); andP. coccineus subsp.polyanthus (no English vernacular name). Biochemical markers—phaseolin seed storage protein and isozymes—have provided new evidence on the organization of the first three species. Domestication has possibly caused a strong reduction in genetic diversity inP. vulgaris andP. acutifolius. BothP. vulgaris andP. lunatus cultivars result from at least two independent domestications, in Mesoamerica and in the Andes. These two species consist of two gene pools, each of which includes wild ancestors and their respective cultivated descendants. Our findings suggest the need for additional emphasis on genetic conservation of wild ancestors and their use in breeding programs and for a comparison of inter-gene pool vs. intra-gene pool crosses in breeding programs.