Genetic diversity and relationships among 192 public common bean inbred lines assessed by SSR markers.

Knowledge of germplasm diversity and of relationships among elite breeding materials has a significant impact on the improvement of crop plants and on the development of strategies for genetic resources management and exploration. The present study was conducted to determine the level of genetic variation and relatedness among some selected common bean varieties by using microsatellite markers. In this investigation, we used 61 SSRs to fingerprint 192 common bean inbred public lines released over the last 50 years in the U.S.A. All the lines are commercial seed type classes that are grown in the USA and include both dry bean classes and snap beans for the fresh and processing markets.The 344 alleles identified were used as raw data for estimating the amount of diversity and to describe the genetic structure of the commercial bean gene pool. A model-based clustering analysis placed the varieties in six clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. Neighbor-joining tree was constructed to further assess the genetic structure of common bean lines, showing good agreement with the pedigree information and the cluster analysis. A significant fixation index FST, also revealed genetic substructure within the U.S. common bean gene pool with Kidney and Pinto-Great Northern beans being the most different from the other varietal groups.The results of this study - based on a much larger number of SSRs -confirm a previous observation indicating a relatively low level of genetic variation and a molecular variability that parallels phenotypic characters distinguishing different commercial groups. Our results indicate also a strong subpopulation structure and provide additional tools for breeding and breeder’s rights implementation

Morphological, biochemical and molecular evaluation of Triticum durum Desf. germplasm.

Durum wheat (Triticum durum Desf., 2n = 4x = 28; AABB genomes) is an important graincrop, particularly in the Mediterranean basin. Over time in Italy plant breeding programs have introduced a number of varieties with always higher and more stable yield and improved grain quality that have continuously replaced the varieties previously locally grown. In order to prevent the genetic erosion of the available durum wheat germplasm, a large number of germplasm collections are currently conserved ex situ in genebanks. Ex situ collections may have a considerable percentage of genetic diversity and useful traits for future breeding needs. So, different approaches can be adopted to explore these germplasm collections. In this study 107 durum wheat accessions collected in Southern Italy and now preserved ex situ in genebanks were characterized. A set of morphological traits (heading date, plant height, spike length, number of spikelet per spike, number of seeds per spike and weight of 1000 seeds) were evaluated. Grain protein content (%) was determined and then gliadins and glutenins patterns were identified by biochemical methods (A-PAGE and SDS-PAGE, respectively). In addition, 30 SSRs markers were used to describe the genetic diversity of the whole collection. According to the plant height, it was possible to divide the collection of accessions into three groups, whose morphological traits reflected the consequences of the introduction of dwarf gene varieties. Grain protein content ranged from 13.6% to 21.7%, with an average of 17.8%. Biochemical characterization of gliadins and glutenins showed a high level of diversity. For gliadins, 100 different bands were identified; 14 patterns were observed in the α region, 23 in the β region, 51 in the γ region and 63 patterns in the ω region. The analysis of the high molecular weight glutenin subunits (HMW-GSs) evidenced that in the collection there were 13 bands and 16 different patterns. The molecular markers identified a total of 115 alleles, with a substantial level of genetic diversity in the whole collection of accessions. The results suggested that genetic diversity was available in the whole germplasm collection,and that the collection can represent a valuable genetic resource for future breeding programs

Identification and characterization in common bean of a putative homologue to the Arabidopsis Indehiscent gene.

Pod shattering represents a key component of the domestication syndrome in common bean, because it makes this species dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene(St) linked to the presence of pod suture fibers involved in pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of the current study was to identify a candidate gene for St. Arabidopsis thaliana INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in Phaseolus vulgaris and mapped on the common bean map using two recombinant inbred population (BAT93 x Jalo EEP558; Midas x G12873). Although PvIND maps near the St locus, the lack of complete co-segregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlating with the dehiscent/indehiscent phenotype suggests that PvIND may be not directly involved in pod shattering and may not be the gene underlying the St locus. Alternatively, a more precise phenotyping method needs to be developed to more accurately map the St locus

Response of Two Local Common Bean Ecotypes of “Fagioli di Sarconi” PGI (Phaseolus vulgaris L.) to Seed-Borne Pathogens and Environmental Change

Among foods protected by the European Union with the PGI (Protected Geographical Indication) mark, several ecotypes of “Fagioli di Sarconi” common beans, typical legumes of Basilicata Region, are included. This work aimed to conduct a survey of seed-borne pathogens isolated from “Ciuoto” and “Cannellino rosso”, ecotypes of “Fagioli di Sarconi” common beans, in two years and cultivation areas of the National Park of the Agri Valley, for identifying resistant and climatic changes well-adapted genotypes. Three validated methods were used for the seed-borne pathogens screening. Eighteen fungi were differently found for ecotype and year of observation by the washing test. Saprophyte contaminants pathogens isolated and detected by the blotter test were strongly reduced by 1% sodium hypochlorite treatment. Using the between paper test, specific for detecting Colletotrichum lindemuthianum, the presence of this pathogen for both ecotypes, years and cultivation areas, and also some bacteria were individuated. Therefore, area-, environment- and ecotype-dependent differences were revealed, probably also caused by a different polyphenolic content and thickness of integument of two ecotypes. This study represents a baseline information for further studies, development of forecasting models and management of seed-borne diseases associated with common beans

Influence of Cultivation Areas on the Seed-Borne Pathogens on Two Local Common Bean Ecotypes of “Fagioli di Sarconi” PGI (Phaseolus vulgaris L.).

Abstract The “Fagioli di Sarconi” common beans, typical of Basilicata Region (Southern Italy), include different ecotypes protected by the European Union with the mark PGI (Protected Geographical Indication). The study aimed to determine the presence of seed-borne pathogens, isolated from two ecotypes of “Fagioli di Sarconi” common beans, “Ciuoto” and “Cannellino rosso”, in two different cultivation areas during the years 2018 and 2019, for identifying genotypes resistant and well adapted to climatic changes. The seeds were evaluated for seed-borne pathogens screening by using three validated seed health testing methods, according to the 2020 International Rules for seed testing. The washing test identified 18 fungal pathogens, different for ecotype and year of observation; the 1% sodium hypochlorite treatment strongly reduced the contaminants. With the blotter test, several saprophyte pathogens were found. Between paper test, specific for detecting the C. lindemuthianum, revealed the presence of this pathogen for both ecotypes and years, in all areas, and individuated some bacteria, too. In conclusion, this work highlighted differences by the two PGI common bean ecotypes in response to seed-borne pathogens resistance and environmental change due probably to their different thickness and polyphenolic content of integument

Genetic diversity and introgression by AFLP analisys in Phaseolus vulgaris L.

Phaseolus vulgaris L. is an economically important species whose origin is in the America continent where domestication took place and diverged in Mesoamerican and Andean gene pools. After Columbus’s voyage common bean was introduced into the Iberian Peninsula from which this species spread into the European countries and around the world. In this study investigate the extent of diversity of European germplasm compared to the American germplasm and to define the level of introgression between the European Mesoamerican and Andean gene pools are investigated. 68 accessions representative of Mesoamerican and Andean American gene pools and 241 accessions from 24 different countries belonging to an European bean core collection were analysed for three morphologic quantitative (length, height and width ) and 4 qualitative (shape, lighter colour, darker colour and coat pattern of seed) seed characters and for 4 AFLP primer combinations: E-AGT/MGAC, E-AGT/M-GTA, E-ACC/M-AGA and E-ACC/M-ATG. A total of 138 polymorphic bands were scored among the 309 accessions analysed. The European and the Mesoamerican gene pools had a number of common and very common AFLP polymorphic bands higher than the American and the Andean gene pools. The European accessions moreover were used for Structure and cpSSR analysis to identify pure and introgressed lines. These groups were compared for morphological traits and AFLP profiles. Results showed significative differences among diverse groups for morphological traits and for AFLP band frequencies, even though the diversity index were the same (He = 0.23). Hypothesis of introgression among American and European, Mesoamerican and Andean gene pools are discussed

Introduction bottleneck and the contribute of Mesoamerican and Andean gene pools to common bean (Phaseolus vulgaris L.) diversity in Europe.

Common bean (Phaseolus vulgaris L., 2n = 2x = 22) is the most important edible food legume for direct human consumption in Europe and in the world as it represents a valuable source of proteins, vitamins, fibres, and minerals. Genetic and archaeological studies have shown that domestication of P. vulgaris was originated and domesticated in the New World and has two major gene pools, the Andean and the Mesoamerican, based on their centers of origin in South and Central America, respectively. After the first voyages of Columbus (1492) common bean was brought to Europe but historical and linguistic sources provide little evidence of the introduction and expansion of common bean in Europe. In common bean a large number of nuclear microsatellite markers (nuSSRs) have been already developed and mapped that show relatively high levels of polymorphism, thus providing an attractive choice for describing population structure. However, to the best of our knowledge, population studies of the European common bean, using nuSSRs, so far have been performed with only a small number of landraces or a small number of samples from a few geographic regions. In the present study, we used thirteen highly polymorphic nuSSRs to assess the genetic structure and level of diversity of a large collection of European landraces (256 individuals), in comparison with a representative American sample (89 individuals). Moreover, to obtain a detailed picture and to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean over the whole Europe, we also complemented the nuSSRs analysis by information provided by a Bayesian analysis implemented in STRUCTURE. Here, we present and discuss the role that inter-gene pool hybridization have had in shaping the genetic structure of the European bean landraces. The implication for evolution and the advantages for common bean breeding are also discussed

Root system architecture phenotyping of durum wheat reveals differential selection for a major QTL in contrasting environments

This study reports the characterization of 183 elite durum wheat (Triticum turgidum ssp. durum Desf.) for RSA and shoot developmental traits. Plants were grown in controlled conditions up to the 7th leaf appearance (late tillering) using the phenotyping platform GROWSCREEN-Rhizo at the Institut f\ufcr Bio und Geowissenschaften Pflanzenwissenschaften

Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Common Bean

The optimal use of legume genetic resources represents a key prerequisite for coping with current agriculture-related societal challenges, including conservation of agrobiodiversity, agricultural sustainability, food security, and human health. Among legumes, the common bean (Phaseolus vulgaris) is the most economically important for human consumption, and its evolutionary trajectories as a species have been crucial to determining the structure and level of its present and available genetic diversity. Genomic advances are considerably enhancing the characterization and assessment of important genetic variants. For this purpose, the development and availability of, and access to, well-described and efficiently managed genetic resource collections that comprise pure lines derived by single-seed-descent cycles will be paramount for the use of the reservoir of common bean variability and for the advanced breeding of legume crops. This is one of the main aims of the new and challenging European project INCREASE, which is the implementation of Intelligent Collections with appropriate standardized protocols that must be characterized, maintained, and made available, along with the related data, to users such as breeders and researchers