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

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

Evaluation of five strategies for obtaining a core subset from a large genetic resource collection of durum wheat.

The use of plant genetic resources contained in a large collection may be enhanced by specifying subsamples, called core samples. Five strategies for selecting a core sample from a collection of 3000 durum wheat accessions were applied and evaluated using four qualitative and eight quantitative spike characters. Each of the following strategies generated about 500 accessions for the core sample: random, random-systematic according to chronology of entry of the accessions into the collection, stratified by countryof-origin, stratified by log frequency by country-of-origin, and stratified by canonical variables. The first three strategies produced samples representative of the whole collection, but the remaining two produced the desired effect of increasing frequencies from less-represented countries-of-origin for several characters. The stratified canonical sample increased phenotypic variances. The quality of core samples is dependent upon good passport and evaluation data to partition the collection. The multivariate approach is extremely useful, but requires considerable data from the whole collection. Ecogeographic origin may be used in the absence of evaluation data on several characters to select useful core samples

Geographical diversity for quantitative spike characters in a world collection of durum wheat.

Crop germplasm collections are formidable to plant breeders and others who wish to draw samples by virtue of their large number of entries and muliplicity of potentially interesting characters. We have examined discriminant and clustering methods for their utility in revealing germplasm groupings that are useful for selection of parental stocks and for revealing evolutionary patterns. More than 3000 entries of durum wheat (Triticum turgidum L., durum group) representing 26 countries of origin were obtained from the U.S. National Small Grains Collection and grown in a common environment in northern California. Eight quantitative measurements on spike characters were made, including awn and spike length, awn/spike length ratio, spikelet number, rachis internode length, number and weight of kernels per spike, and mean single kernel weight. Five clusters were delineated among the 26 country origins: (i) 11 countries in Europe and North Africa; (ii) France, USSR, and USA; (iii) nine countries in the eastern Mediterranean area; (iv) Ethiopia and India; (v) Afghanistan. An east to west clinal pattern was detected that represents a gradient in unimproved to improved types. Some countries with contrasting agroecological conditions clustered together, probably because a high percentage of breeding lines and cultivars shared parents from among the clustered countries. These results revealed wide variation in numbers of entries from among countries. Certain areas should be sampled morextensively. Documentation data are less complete than desired to establish evolutionary and ecological relationships. The methods used here helped focus upon groups of materials for use in plant breeding and research