Morphological Diversity of Tropical Common bean Germplasm

Common bean ( Phaseolus vulgaris L.) landraces and varieties grown by farmers in the tropics are a major source of genes and genetic diversity for bean improvement. These materials are, however, threatened by genetic erosion. In this study, we sought to understand the current state of genetic diversity of common bean in Uganda, using the available collection consisting of 284 bean accessions. A field experiment was conducted at the National Crops Resources Research Institute in Namulonge, Uganda. The level of morphological variation estimated with the Shannon Weaver diversity index (H), ranged from 0.47 to 0.58, with an overall mean of 0.56\ub10.19, an indicator of moderate genetic diversity. Principal component analysis (PCA) clustered the germplasm into three major groups (G1, G2 and G3). The genotypes differed mostly for growth habit, pod cross-section, pod curvature, hypocotyl colour, days to flowering, node number on the main stem, number of flower buds, and 100 seed weight.Les cultivars et vari\ue9t\ue9s de haricot commun ( Phaseolus vulgaris L.) cultiv\ue9s par les fermiers dans les tropiques son tune source majeur de \ue8nes et diversit\ue9 g\ue9n\ue9tique pour l\u2019am\ue9lioration du haricot. Ce materiel est, par ailleurs, handicap\ue9 par une \ue9rosion g\ue9n\ue9tique. Le but de cette \ue9tude est de comprendre la situation courante de la diversit\ue9 g\ue9n\ue9tique du haricot commun en Ouganda, en utilisant la collection disponible de 284 accessions de haricots. Un essai \ue9tait conduit au National Crops Resources Research Institute \ue0 Namulonge, Ouganda. Le niveau de variation morphologique estim\ue9 \ue0 l\u2019aide de l\u2019indice de diversit\ue9 de Shannon Weaver (H),variait de 0.47 \ue0 0.58, avec une moyenne g\ue9n\ue9rale de 0.56\ub10.19, un indicateur de diversit\ue9 g\ue9n\ue9tique mod\ue9r\ue9. L\u2019analyse de la composante principale (PCA) a group\ue9 le germplasme en trois groupes majeurs (G1, G2 et G3). Les g\ue9notypes differaient plus par l\u2019habitude de croissance, la section des gousses, la courbature des gousses, la couleur de l\u2019hypocotyle, les jours \ue0 la floraison, le nombre de nodes sur la tige principale, le nombre de bourgeon des fleurs et le poids de 100 graines

AGRONOMIC QUALITIES OF GENETIC PYRAMIDS OF COMMON BEAN DEVELOPED FOR MULTIPLE-DISEASE-RESISTANCE

Multiple co-infections by different pathogens on common bean ( Phaseolus vulgaris L.) affect its productivity and cause complete crop loss in susceptible varieties. Therefore, gene pyramiding using marker assisted selection (MAS) and backcrossing, provide alternative cost-effective control measures to bean diseases. However, in the process of developing pyramids, linkage drags were likely to affect the qualities of progeny lines, hence, special attention was paid to this situation. The objective of this study was thus to assess the agronomic qualities of advanced genetic pyramids developed from a four-way cross for multiple disease resistance. The disease resistance genes (R) pyramided from four parents were: Co42 and Co-5 from G2333; Phg-2 from MEX54; Pythium ultimum Dennis from MLB49-89A and I & bc3 from MCM5001. The progeny lines were planted in an incomplete block design, and replicated thrice for two seasons (2015A and 2015B) in fields at CIAT, Kawanda in Uganda. Agronomic traits were highly heritable (0.6), except number of pods per plant (< 0.3). Backcrossing generated high-yielding bean lines, with 270 - 290 seed per plant and early maturity (95-100 days). Nine superior lines with desirable qualities, such as earliness (95 days), high seed rate (290 seeds per plant), and climbing ability, were obtained. Pyramiding R genes did not affect yield traits, except time to flowering and number of flower buds per plant due to transgressive segregation.Les co-infections multiples par de diff\ue9rents pathog\ue8nes sur le haricot commun ( Phaseolus vulgaris L.) affectent sa productivit\ue9 et causent la perte totale des vari\ue9t\ue9s susceptibles de la culture. Par cons\ue9quent, la pyramide des g\ue8nes en utilisant la s\ue9lection assist\ue9e par des marqueurs (MAS) et le r\ue9trocroisement, fournissent des mesures alternatives de contr\uf4le moins ch\ue8res des maladies du haricot. N\ue9anmoins, dans le processus du d\ue9veloppement des pyramides, les poids des liaisons affectent probablement les qualit\ue9s des lign\ue9es de prog\ue9nitures, de ce fait, une attention particuli\ue8re \ue9tait port\ue9e \ue0 cette situation. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer les qualit\ue9s agronomiques des pyramides g\ue9n\ue9tiques avanc\ue9es d\ue9velopp\ue9es d\u2019un croisement de quatre parents pour la r\ue9sistance aux maladies multiples. Les g\ue8nes pyramid\ue9s de r\ue9sistance (R) \ue0 la maladie de quatre parents \ue9taient\ua0: Co42 et Co-5 de G2333; Phg-2 de MEX54; Pythium ultimum Dennis de MLB49-89A et I & bc3 de MCM5001. Les lign\ue9es de prog\ue9nitures \ue9taient plant\ue9es en arrangement de block incomplet et r\ue9pliqu\ue9 trois fois pendant deux saisons (2015A et 2015B) dans les champs \ue0 CIAT, Kawanda en Ouganda. Les traits agronomiques \ue9taient hautement h\ue9ritables (0,6), \ue0 l\u2019exception du nombre de gousses par plant (<0.3). Le r\ue9trocroisement a g\ue9n\ue9r\ue9 des lign\ue9es d\u2019haricot \ue0 haut rendement, avec 270-290 graines par plant et \ue0 maturit\ue9 pr\ue9coce (95-100 jours). Neuf lign\ue9es sup\ue9rieures avec des qualit\ue9s d\ue9sirables, telles que la pr\ue9cocit\ue9 (95 jours), taux de graines \ue9lev\ue9s (290 graines par plant) et l\u2019habilit\ue9 grimpante, \ue9taient obtenues. La pyramide des g\ue8nes R n\u2019avait pas affect\ue9 les traits li\ue9s au rendement, \ue0 l\u2019exception de la p\ue9riode de floraison et le nombre de bougeons de fleurs par plant d\ufb \ue0 la s\ue9gr\ue9gation transgressive

Identification and Validation of Novel Cerebrospinal Fluid Biomarkers for Staging Early Alzheimer's Disease

Ideally, disease modifying therapies for Alzheimer disease (AD) will be applied during the 'preclinical' stage (pathology present with cognition intact) before severe neuronal damage occurs, or upon recognizing very mild cognitive impairment. Developing and judiciously administering such therapies will require biomarker panels to identify early AD pathology, classify disease stage, monitor pathological progression, and predict cognitive decline. To discover such biomarkers, we measured AD-associated changes in the cerebrospinal fluid (CSF) proteome.CSF samples from individuals with mild AD (Clinical Dementia Rating [CDR] 1) (n = 24) and cognitively normal controls (CDR 0) (n = 24) were subjected to two-dimensional difference-in-gel electrophoresis. Within 119 differentially-abundant gel features, mass spectrometry (LC-MS/MS) identified 47 proteins. For validation, eleven proteins were re-evaluated by enzyme-linked immunosorbent assays (ELISA). Six of these assays (NrCAM, YKL-40, chromogranin A, carnosinase I, transthyretin, cystatin C) distinguished CDR 1 and CDR 0 groups and were subsequently applied (with tau, p-tau181 and Aβ42 ELISAs) to a larger independent cohort (n = 292) that included individuals with very mild dementia (CDR 0.5). Receiver-operating characteristic curve analyses using stepwise logistic regression yielded optimal biomarker combinations to distinguish CDR 0 from CDR>0 (tau, YKL-40, NrCAM) and CDR 1 from CDR<1 (tau, chromogranin A, carnosinase I) with areas under the curve of 0.90 (0.85-0.94 95% confidence interval [CI]) and 0.88 (0.81-0.94 CI), respectively.Four novel CSF biomarkers for AD (NrCAM, YKL-40, chromogranin A, carnosinase I) can improve the diagnostic accuracy of Aβ42 and tau. Together, these six markers describe six clinicopathological stages from cognitive normalcy to mild dementia, including stages defined by increased risk of cognitive decline. Such a panel might improve clinical trial efficiency by guiding subject enrollment and monitoring disease progression. Further studies will be required to validate this panel and evaluate its potential for distinguishing AD from other dementing conditions

A review of angular leaf spot resistance in common bean.

Angular leaf spot (ALS), caused by Pseudocer-cospora griseola, is one of the most devastating diseases of common bean (Phaseolus vulgarisL.) in tropical and subtropical production areas. Breeding for ALS resistance is difficult due to the extensive virulence diversity of P. griseolaand the recurrent appearance of new virulent races. Five major loci, Phg-1 to Phg-5, confer-ring ALS resistance have been named, and markers tightly linked to these loci have been reported. Quantitative trait loci (QTLs) have also been described, but the validation of some QTLs is still pending. The Phg-1, Phg-4, and Phg-5loci are from common bean cultivars of the Andean gene pool, whereas Phg-2 and Phg-3are from beans of the Mesoamerican gene pool. The reference genome of common bean and high-throughput sequencing technologies are enabling the development of molecular markers closely linked to the Phg loci, more accurate mapping of the resistance loci, and the compar-ison of their genomic positions. The objective of this report is to provide a comprehensive review of ALS resistance in common bean. Further-more, we are reporting three case studies of ALS resistance breeding in Latin America and Africa. This review will serve as a reference for future resistance mapping studies and as a guide for the selection of resistance loci in breeding programs aiming to develop common bean cultivars with durable ALS resistance

The genetic diversity and population structure of common bean (Phaseolus vulgaris L) germplasm in Uganda

The knowledge and understanding of the genetic variability of common bean (Phaseolus vulgaris L.) germplasm is important for the implementation of measures addressed to their utilizations and conservation. The objective of this study was to characterize common bean in Uganda using polymorphic molecular markers for use in hybridization and variety development. Genomic DNA was extracted from plants at the first trifoliate leaf stage growing in pots using the modified cetyl-trimethylammonium bromide (CTAB) method. The gene pool membership (Andean vs. Mesoamerican) for each accession was established with the phaseolin marker. Simple sequence repeat (SSR) alleles were separated by capillary electrophoresis that provided further information on the organization of genetic diversity. The Andean and Mesoamerican genotypes were present in similar frequencies (51 vs. 49%, respectively). All SSR markers tested were polymorphic with mean polymorphism information content (PIC) of 0.8. The model-based cluster analysis of SSR diversity in the STRUCTURE software found three sub populations (K3.1, K3.2 and K3.3) genetically differentiated with moderate Wrights fixation indices (FST) values 0.14, 0.12 and 0.09, respectively and many cases of admixture. The STRUCTURE result was confirmed by Principal Coordinate analysis (PCoA) which also clustered beans in three groups. Most Andean genotypes were included in K3.1 and Mesoamerican genotypes belonged to the K3.2 and K3.3 subgroups. This study sets the stage for further analyses for agronomic traits such as yield, resistance to biotic and abiotic stresses and the need for germplasm conservation.Keywords: Phaseolin, Simple sequence repeat (SSR), hybridization, wrights fixation index (FST), structure.African Journal of Biotechnology, Vol 13(29) 2935-294

Agronomic qualities of genetic pyramids of common bean developed for multiple-disease-resistance

Multiple co-infections by different pathogens on common bean (Phaseolus vulgaris L.) affect its productivity and cause complete crop loss in susceptible varieties. Therefore, gene pyramiding using marker assisted selection (MAS) and backcrossing, provide alternative cost-effective control measures to bean diseases. However, in the process of developing pyramids, linkage drags were likely to affect the qualities of progeny lines, hence, special attention was paid to this situation. The objective of this study was thus to assess the agronomic qualities of advanced genetic pyramids developed from a four-way cross for multiple disease resistance. The disease resistance genes (R) pyramided from four parents were: Co42 and Co-5 from G2333; Phg-2 from MEX54; Pythium ultimum Dennis from MLB49-89A and I & bc3 from MCM5001. The progeny lines were planted in an incomplete block design, and replicated thrice for two seasons (2015A and 2015B) in fields at CIAT, Kawanda in Uganda. Agronomic traits were highly heritable (0.6), except number of pods per plant (< 0.3). Backcrossing generated high-yielding bean lines, with 270 - 290 seed per plant and early maturity (95-100 days). Nine superior lines with desirable qualities, such as earliness (95 days), high seed rate (290 seeds per plant), and climbing ability, were obtained. Pyramiding R genes did not affect yield traits, except time to flowering and number of flower buds per plant due to transgressive segregation

Common Bean variety releases in Africa

The Pan Africa Bean Research Alliance is a network of national agricultural research centers (NARS), and private and public sector institutions that work to deliver better beans with consumer and market preferred traits to farmers. The datasets presented here draw from 17 Sub Saharan countries that are members of PABRA. The dataset on released bean varieties is a collection of 513 bean varieties released by NARS and there characteristics. The dataset on bean varieties and the relationship to constraints provides the 513 bean varieties on the basis of resistance to constraints such as fungal, bacterial, viral, diseases and tolerance to abiotic stresses. There is also a dataset of bean varieties that have been released in more than one country, useful for moving seed from one country to another and facilitating regional trade. The dataset on Niche market traits provides the market defined classifications for bean trade in Sub Saharan Africa as well as varieties that fall into these classifications. The datasets are an update to the 2011 discussion on PABRAs achievement in breeding and delivery of bean varieties in Buruchara et. 2011 in pages 236 and 237 here: http://www.ajol.info/index.php/acsj/article/view/74168 . It is also an update to a follow up to this discussion in Muthoni, R. A., Andrade, R. 2015 on the performance of bean improvement programmes in sub-Saharan Africa from the perspectives of varietal output and adoption in chapter 8. here: http://dx.doi.org/10.1079/9781780644011.0148. The data is extracted from the PABRA M&E database available here (http://database.pabra-africa.org/?location=breeding)

Common Bean variety releases in Africa

The Pan Africa Bean Research Alliance is a network of national agricultural research centers (NARS), and private and public sector institutions that work to deliver better beans with consumer and market preferred traits to farmers. The datasets presented here draw from 17 Sub Saharan countries that are members of PABRA. The dataset on released bean varieties is a collection of 357 bean varieties released by NARS and there characteristics. The dataset on bean varieties and the relationship to constraints provides the 357 bean varieties on the basis of resistance to constraints such as fungal, bacterial, viral, diseases and tolerance to abiotic stresses. There is also a dataset of bean varieties that have been released in more than one country, useful for moving seed from one country to another and facilitating regional trade. The dataset on Niche market traits provides the market defined classifications for bean trade in Sub Saharan Africa as well as varieties that fall into these classifications. The datasets are an update to the 2011 discussion on PABRAs achievement in breeding and delivery of bean varieties in Buruchara et. 2011 in pages 236 and 237 here: http://www.ajol.info/index.php/acsj/article/view/74168 . It is also an update to a follow up to this discussion in Muthoni, R. A., Andrade, R. 2015 on the performance of bean improvement programmes in sub-Saharan Africa from the perspectives of varietal output and adoption in chapter 8. here: http://dx.doi.org/10.1079/9781780644011.0148. The data is extracted from the PABRA M&E database available here ( http://database.pabra-africa.org/?location=breeding)