SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad

POTENSI ANTIOKSIDAN DAN KADAR TOTAL FENOL TEMPE KACANG MERAH (Phaseolus vulgaris l.), KACANG TANAH (Arachis hypogeae l.) DAN KACANG KEDELAI (Glycine max)

Pendahuluan: Tempe adalah olahan makanan dari fermentasi kacang – kacangan khas Indonesia dan mempunyai efek antioksidan. Produk tempe menggunakan bahan dasar kacang kedelai (Glycine max) atau bahan lain seperti kacang tanah (Arachis hypogaea L.) dan kacang merah (Phaseolus vulgaris L.). Kacang – kacangan tersebut memiliki nilai gizi tinggi dan aktivitas antioksidan tinggi. Dengan demikian penelitian untuk mengkaji potensi antioksidan tempe berbahan dasar ketiga kacang sangat penting dilakukan. Penelitian ini betujuan untuk mengetahui perbedaan kadar total fenol dan aktivitas antioksidan tempe Phaseolus vulgaris, Arachis hypogaea dan Glycine max.Metode: Penelitian ini menggunakan metode in vitro dengan menguji ekstrak etanoltempe Phaseolus vulgaris, Arachis hypogaea dan Glycine max terhadap kadar total fenolnya menggunakan metode Folin-Ciaocalteu. Serta menguji aktivitas antioksidannya menggunakan metode DPPH (2,2-diphenyl- 1-picrylhydracyl radical). Analisis statistik data menggunakan aplikasi SPSS versi 22 pada uji one way ANOVA.Hasil: Hasil penelitian menunjukkan kadar total fenol pada tempe Phaseolus vulgaris, Arachis hypogaea dan Glycine max yaitu 107,88±1,55 ; 3,11±1,27; 43,91±1,16 mg GAE/g (p≤0.05) dan aktivitas antioksidan dilihat dari nilai IC50 yaitu 312,12 ; 560,23; 623,14 μg/mL (p≤0.05). Hasil IC50 pada vitamin C sebagai kontrol pembanding, hasilnya lebih rendah dari ketiga jenis tempe tersebut (0,62 μg/mL). Vitamin C memiliki aktivitas antioksidan tertinggi.Simpulan: Tempe berbahan dasar Phaseolus vulgaris mempunyai kadar fenol dan aktivitas antioksidan tertinggi dibandingkan dengan tempe Arachis hypogaea dan Glycine max. Kata Kunci: Tempe Phaseolus vulgaris L., Tempe Arachis hypogaea L., Tempe Glycine max, Antioksidan.

Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

Abstract Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris , the progenitor of common bean ( P. vulgaris ), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for ∼20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris . As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean. Author Summary The ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from ∼35° N. Lat. to ∼35° S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method – outlier detection – was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method – genome-wide association – was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans

ANТIGENS STRUCTURE OF ТНЕ PHYTOHEMAGGLUТININ OF PHASEOLUS VULGARIS

Phytohemagglutinins (РНА) are considered and utilized chiefly as antibodies in the field of experimental and аррlied medicine.Dujarrie de la Riuier and associates are the first to put in the problem as а matter of principle for the antigenic properties in the РНА and carry out experimental studies under this aspect.With renewed interest the question of the antigenic properties of РНА from Phaseolus vulgaris was raised after discovering its mitogenic abllity upon leukocytes of the human peripheric blооd in vitro. Pearmain and associates are the first to postulate the hypothesis that this phenomenon represents an immunological reaction of the leukocytes to the special РНА antigenic properties.We obtained РНА from the seeds of various types Phaseolus vulgaris, among which we chose the one with the most powerfully manifested mitogenetic properties. The РНА thus obtained represents purified globulin fractions, as already established bу the same authors in earlier investigations.Proving the antigenic structure of the РНА from Phaseolus vulgaris surges а particular scientific interest in the process of studying the essentials of its mitogenetic capacity. In our present work we give an account of the results btained from investigations on the antigenic structure of РНА of Phaseolus vulgaris. The experimentation was carried out in accordancewith the following plan: 1) determination of the antigenic structure of РНА from Phaseolus vulgaris, type Saxa and their identity with the antigens of РНА from the other sorts of this type; 2) determination of the antigens of РНА from Phaseolus vulgaris, sort Saxa and their related antigens in РНА obtained from the seeds of other sorts of the family Leguminosae - peas, soy-bean and hatchet.

Detection of two endornavirus in common bean genotypes in Brazil.

Endornaviruses (Endornaviridae) are persistent viruses that infect important crops such as pepper, rice, broad bean, and beans. However, these viruses are poorly studied and have not yet been reported in Brazil. In this study, we investigated the occurrence of two endornaviruses, Phaseolus vulgaris endornavirus-1 (PvEV-1) and Phaseolus vulgaris endornavirus-2 (PvEV-2) in bean genotypes

Culinary and sensory traits diversity in the Spanish Core Collection of common beans (Phaseolus vulgaris L.)

The Spanish National Plant Genetic Resource Center's core collection of bean germplasm includes 202 accessions selected from more than 3000 accessions in function of passport data, seed phenotype, genetic background, and agronomic traits. To acquire more useful information about these accessions, we cultivated and characterized them for sensory and culinary traits. We found considerable variation for culinary and sensory traits of the cooked beans (mean coefficients of variation: 41% for the sensory traits and 40% for the culinary traits). The large dataset enabled us to study correlations between sensory and culinary traits and among these traits and geographic origin, seed color, and growth habit. Greater proportion of white in the seed coat correlated positively with brightness and negatively with mealiness (r=0.60, r=-0.60, p<0.001, respectively). Mealiness correlated negatively with seed-coat roughness and rate of water absorption (r=-0.60, r=-0.53, p<0.001, respectively). Materials of Andean origin had lower seed-coat brightness (p<0.01) and seed-coat roughness, and greater seed-coat perceptibility, mealiness, flavor, and aroma (p<0.001) than materials of Mesoamerican origin. Growth habit failed to correlate with culinary or sensory traits.Postprint (published version

Studies on the major seed proteins of some grain crops

The general properties, classification and distribution of plant proteins are discussed within an agricultural context and the protein content and composition of several grain crops are tabulated. The major proteins of legume seeds are salt soluble proteins (i.e. globulins) and the methodology for their extraction, separation and characterisation is reviewed. The structure, location and distribution of legume globulins are described and the properties of various purified legume globulins are compared. The major seed proteins of Pisum sativum are legumin and vicilin and seed globulins with properties similar to those of legumin and vicilin have been extracted from other legumes. The isolation and partial characterisation of vicilin-like proteins from seeds of Phaseolus vulgaris and Vigna vinguiaulata and of legumin-like proteins from these two species and Phaseolus aureus is described. The potential usefulness of the examination of seed proteins by polyacrylamide gel electrophoresis to taxonomic problems in Phaseolus and Vigna is investigated and the data obtained are discussed in relation to recent re-classifications of the species. Procedures for the extraction and partial characterisation of proteins from an archaeological sample of maize grains are described and the proteins from this sample are compared with the proteins from a modern variety of maize. It is suggested that protein data from archaeological samples could be useful in studies of crop plant origins and in cultural studies, and that the procedures employed may be applicable to archaeological samples of other grains. Nutritional aspects of plant proteins are discussed briefly. A possible strategy for the improvement of the sulphur amino acid content of legumes with a relatively low legumin content is suggested and it is demonstrated that polyacrylamide gel electrophoresis may provide a basis for a screening procedure for protein quality in legume breeding programmes

Germplasm identification of bean ( Phaseolus vulgaris L.) and lettuce ( Lactuca sativa L.) resistant to avirulent populations of Meloidogyne spp. to Mi gene

Phytoparasitic nematodes of the genus Meloidogyne spp. are the cause of important losses in horticulture. In recent years, plant resistance has been used to reduce this damage in a sustainable way. The present work determines the resistance against Meloidogyne spp. of two varieties of lettuce Grand Rapids and Salinas 88, and the resistance of three varieties of common bean Aporé, Macarrão Atibaia and Ouro Negro, which have previously been studied in the University Federal University of Lavras (UFLA), Brazil. Furthermore this study will assess the possibility of resistance of a common bean cultivar, Cornell 49242, which has not been previously tested. As a method of controlling all the tests carried out two cultivars were used - Regina 71 for lettuce and Bolinha for common bean. In order to characterize the resistance, two experiments were carried out. Firstly, both crops were confronted with 11 populations of Meloidogyne incognita and M. javanica in a pot experiment. Secondly, a field conditions experiment was used to observe the behaviour of the different cultivars under different densities of Meloidogyne incognita. The results confirmed the resistance of the Grand Rapids and Salinas 88 lettuce cv to nematode populations from Almeria, Murcia and Catalonia., as they obtained lower nematode reproductions in the pot experiment and reduced the soil population in the field experiment. The common bean cultivars showed more diverse results. Aporé cv. proved to be resistant in all experiments. The results for Macarrão Atibaia and Ouro Negro showed their slight resistance and susceptibility (of the 45%) to the majority of the nematode populations used in the pot experiment. In field conditions the results differed. Ouro Negro was slightly resistant, but Macarrão Atibaia behaved as susceptible with an 81.9% of reproduction compared to Bolinha (susceptible cultivar of control). The cultivar Cornell 49242 behaved as susceptible in front the majority of the Meloidogyne spp. populations of the pot experiment.Meloidogyne spp. és un gènere de nematodes fitoparàsits causant de pèrdues importants en horticultura. En els darrers anys s'ha utilitzat la resistència vegetal per a controlar el nematode de forma sostenible. En el present treball es determina la resistència vegetal en front Meloidogyne spp. de dues varietats d'enciam Grand Rapids i Salinas 88, i de tres varietats de mongeta Aporé, Macarrão Atibaia i Ouro Negro, de les quals s'han realitzat treballs previs a la Universitat Federal de Lavras (UFLA) , Brasil. També s'avalua la possible resistència d'una varietat de mongeta, Cornell 49242, no caracteritzada prèviament. Com a control de tots els assajos portats a terme s'han utilitzat la varietat susceptible d'enciam Regina 71, i de mongeta Bolinha. Per a la caracterització de la resistència es va realitzar un experiment en torretes per cada cultiu en el que es va enfrontar les diferents varietats a 11 poblacions de Meloidogyne incognita i M. javanica; i un experiment en condicions de camp on es va avaluar el comportament de les diferents varietats davant diferents densitats de Meloidogyne incognita. Els resultats van confirmar la resistència per a poblacions de nematodes provinents d'Almería, Murcia i Catalunya de les varietats d'enciam Grand Rapids i Salinas 88, obtenint reproduccions inferiors del nematode en l'experiment en torretes i reduint la població en el sòl en l'experiment de camp. Les varietats de mongeta varen tenir resultats més variables. El cultivar Aporé es va mostrar resistent en tots els assajos. Macarrão Atibaia i Ouro Negro es van mostrar com a lleugerament resistents i susceptibles (45%), en front la majoria de poblacions de nematodes utilitzades en l'assaig en torreta. En camp, Ouro Negro es va mostrar lleugerament resistent, però Macarrão Atibaia es va comportar com a susceptible amb un 81.9% de reproducció respecte Bolinha (varietat susceptible de control). El cultivar Cornell 49242 es comportar com a susceptible en front la majoria de poblacions de Meloidogyne spp. en l'assaig de torreta.Meloidogyne spp. Es un género de nematodos fitoparásitos causante de pérdidas importantes en horticultura. En los últimos años se ha utilizado la resistencia vegetal a fin de reducir los daños causados de forma sostenible. En el presente trabajo se determina la resistencia frente Meloidogyne spp. de dos variedades de lechuga Grand Rapids y Salinas 88, y tres variedades de judía Aporé, Macarrão Atibaia y Ouro Negro, de las que se han realizado trabajos previos a la Universidad Federal de Lavras (UFLA), Brasil. También se evalúa la posible resistencia de una variedad de judía, Cornell 49242, no caracterizada previamente. Como control de todos los ensayos llevados a cabo se han utilizado las variedades susceptibles Regina 71, por lechuga y Bolinha, por judía. Para la caracterización de la resistencia se realizó un experimento en macetas para cada cultivo en el que se enfrentó las diferentes variedades a 11 poblaciones de Meloidogyne incognita y M. javanica; y un experimento en condiciones de campo donde se evaluó el comportamiento de las diferentes variedades ante diferentes densidades de Meloidogyne incognita. Los resultados confirmaron la resistencia para poblaciones de nematodos provenientes de Almería, Murcia y Cataluña de las variedades de lechuga Grand Rapids y Salinas 88, obteniendo reproducciones inferiores del nematodo en el experimento en macetas y reduciendo la población del suelo en el experimento de campo. Las variedades de judía tuvieron resultados más variables. El cultivar Aporé se mostró resistente en todos los ensayos. Macarrão Atibaia y Ouro Negro se mostraron como ligeramente resistentes y susceptibles (45%), frente a la mayoría de poblaciones de nematodos en el ensayo en maceta. En campo, Ouro Negro se mostró ligeramente resistente, pero Macarrão Atibaia se comportó como susceptible con un 81.9% de reproducción respecto Bolinha (variedad susceptible de control). El cultivar Cornell 49242 se comportó como susceptible frente la mayoría de poblaciones de Meloidogyne spp. en el ensayo de macetas