Dataset Information

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

ABSTRACT: Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

SUBMITTER: Gioia T

PROVIDER: S-EPMC6354994 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

Gioia Tania T Logozzo Giuseppina G Marzario Stefania S Spagnoletti Zeuli Pierluigi P Gepts Paul P

PloS one 20190131 1

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and in ...[more]

PMID: 30703134

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Project description:BackgroundGene-based (genic) microsatellites are a useful tool for plant genetics and simple sequence repeat loci can often be found in coding regions of the genome. While EST sequencing can be used to discover genic microsatellites, direct screening of cDNA libraries for repeat motifs can save on overall sequencing costs. The objective of this research was to screen a large cDNA library from and Andean common bean genotype for six di-nucleotide and tri-nucleotide repeat motifs through a filter hybridization approach and to develop microsatellite markers from positive clones.ResultsRobotics were used for high-throughput colony picking and to create a high-density filter of 18,432 double spotted cDNA clones which was followed by hybridization with repeat motif containing probes based on GA, CA, AAT, CAG, CAA and ACG repeats. A total of 1203 positive clones were identified by their addresses and sequenced from 5' ends and if required from 3' ends to confirm repeat motif and length. Out of 886 high quality sequences, 497 had complete microsatellite loci that were not truncated by the sequencing reaction and of these tri-nucleotide repeats were more common than di-nucleotide repeats. Different motifs were found in different frequencies in the 5' and 3' ends of the cDNAs. In a microsatellite development program, primers were designed for 248 SSR loci which were tested on a panel of 18 common bean genotypes to determine their potential as genetic markers finding higher average polymorphism information content for di-nucleotide repeat markers (0.3544) than for tri-nucleotide repeat markers (0.1536).ConclusionThe present study provides a set of validated gene-based markers for common bean that are derived from G19833, an Andean landrace that is an important source of disease and abiotic stress tolerance which has been used for physical map development and as a mapping parent. Gene-based markers appear to be very efficient at separating divergent wild and cultivated accessions as well as Andean and Mesoamerican gene pools and therefore will be useful for diversity analyses and for comparative and transcript mapping in common bean.

Project description:BACKGROUND:Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS:An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS:Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS:The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

Project description:Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Project description:Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.

Dataset Information

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

Publications

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

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