Association Studies and Legume Synteny Reveal Haplotypes Determining Seed Size in Vigna unguiculata.

Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes. Allelic variation dictating the inheritance of seed size can be tagged and used to assist the selection of large seeded lines. In this work we applied 1,536-plex SNP genotyping and knowledge of legume synteny to characterize regions of the cowpea genome associated with seed size. These marker-trait associations will enable breeders to use marker-based selection approaches to increase the frequency of progeny with large seed. For 804 individuals derived from eight bi-parental populations, QTL analysis was used to identify markers linked to 10 trait determinants. In addition, the population structure of 171 samples from the USDA core collection was identified and incorporated into a genome-wide association study which supported more than half of the trait-associated regions important in the bi-parental populations. Seven of the total 10 QTLs were supported based on synteny to seed size associated regions identified in the related legume soybean. In addition to delivering markers linked to major trait determinants in the context of modern breeding, we provide an analysis of the diversity of the USDA core collection of cowpea to identify genepools, migrants, admixture, and duplicates

Facteurs associés à la dissociation immunovirologique chez les patients infectés par le VIH-1 sous traitement antirétroviral hautement actif au Centre de Traitement Ambulatoire (CTA) de Dakar

Introduction: L'objectif de ce travail était d'évaluer les différents facteurs associés à la dissociation immunovirologique malgré un traitement antirétroviral hautement actif et efficace.Méthodes: Il s'agissait d'une étude de cohorte historique, descriptive et analytique faite à partir de dossiers de patients infectés par le VIH-1; sous traitement antirétroviral depuis au moins 12 mois, suivis dans la cohorte du CTA de 2001 à 2011 et ayant une charge virale indétectable depuis 6 mois.Résultats: Durant cette période d'étude de 10 ans, la prévalence de la DIV était de 19,3%. Le sexe féminin était prédominant avec un sexe ratio de 1,9. La dissociation immunovirologique a été plus fréquemment rencontrée chez les patients de sexe masculin (29,7% vs 14,1%) avec une différence statistiquement significative (p = 0,00006). L'âge médian était de 44 ans ± 10 ans. Un antécédent de tuberculose a été retrouvé dans environ un tiers des cas (31,4%). La dissociation immunovirologique était significativement plus fréquente chez les patients ayant un antécédent de tuberculose (p = 0,00005). La plupart des patients (68%) était au stade SIDA 3 ou 4 de l'OMS. Les patients ayant une dissociation immunovirologique étaient plus souvent aux stades 3 et 4 de l'OMS (p = 0,0001). La dénutrition a été notée dans plus de la moitié des cas (56,2%) et la dissociation immunovirologique prédominait chez les patients dénutris (p=0,005). Le taux moyen de lymphocytes TCD4+ était de 86,7± 83 cellules / mm3. La dissociation immunovirologique était plus fréquente chez les patients ayant un taux de lymphocytes TCD4 bas à l'initiation avec une différence statistiquement significative (p = 0,00000). En analyse multivariée; Seuls l'âge supérieur ou égal à 43 ans, le taux de CD4 initial < 100 c/mm3 et le sexe masculin étaient significativement associés à cette dissociation immunovirologique.Conclusion: Les principaux facteurs associés à la dissociation immunovirologique étant évalués, d'autres études portant sur ce groupe mériteraient d'être envisagées afin de connaitre l'impact de cette réponse immunologique partielle sur la survenue d'infections opportunistes ou bien la mise en place d'une trithérapie spécifique uniquement dans le but d'avoir une restauration immunologique optimale.Mots clés: Dissociation, immunovirologique, VIH, DakarEnglish Title: Factors associated with immunovirologic dissociation in HIV-1-infected patients under highly active antiretroviral therapy in the Ambulatory Treatment Center (ATC) in DakarEnglish AbstractIntroduction: the objective of this work is to evaluate the different factors associated with immunovirologic dissociation despite highly active and effective antiretroviral treatment.Methods: we conducted a retrospective, cohort, descriptive and analytical study of the medical records of HIV-1 infected patients having received at least 12 months of antiretroviral therapy, followed in the ATC cohort from 2001 to 2011 and with undetectable viral load in the last 6 months.Results: during this 10-year study period, the prevalence of IVD was 19.3%. Female sex was predominant, with a sex ratio of 1.9. Immunovirologic dissociation was more frequent in male patients (29.7% vs 14.1%) with a statistically significant difference (p = 0,00006). The average age was 44 years ± 10 years. A history of tuberculosis was found in about a third of the cases (31.4%). Immunovirologic dissociation was significantly more frequent in patients with a history of tuberculosis (p = 0.00005). Most patients (68%) had AIDS at WHO clinical stages 3 or 4. Patients with immunovirologic dissociation were more often in WHO clinical stages 3 and 4 (p = 0.0001). More than half of the cases (56.2%) were found to be malnourished and immunovirologic dissociation was prevalent in malnourished patients (p=0.005). The mean CD4+ T lymphocytes counts was 86.7± 83 cells / mm3. Immunovirologic dissociation was more frequent in patients with initial low CD4+ T lymphocyte counts and with a statistically significant difference (p = 0.00000). By multivariate analysis, only age greater than or equal to 43 years, CD4 initial counts < 100 c/mm3 and male sex were significantly associated with this immunovirologic dissociation.Conclusion: our study assessed the main factors associated with immunovirologic dissociation. Other studies of this nature would also merit consideration in order to highlight the impact of this partial immune response on the emergence of opportunistic infections or the implementation of a specific tritherapy for the sole purpose of producing fully successful immune restoration.Keywords: Dissociation, immunovirologic, HIV, Daka

Genome Resources for Climate‐Resilient Cowpea, an Essential Crop for Food Security

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited‐input small‐holder farming and climate stress

Genotype x row spacing and environment interaction of cowpea in semi-arid zones

Row spacing x genotype interaction caused by changes in genotype ranking could require twice the resources to identify superior genotypes. This study was conducted to estimate the magnitude of genotype x row spacing interaction and its effects on testing and selection procedures used in cowpea (Vigna unguiculata L. Walp) cultivar development. Ten genotypes were evaluated for grain yield and harvest index with 50 x 50 and 50 x 25 cm spacings, for two years at two locations. Within row spacing (WRS) did not have a significant effect on either trait. Genotype x within row spacing interaction effects were not significant, suggesting that selection at low densities would be effective in identifying superior and productive genotypes for further testing in either within row spacing. Because of significant genotype x environment and WRS interaction effects, this effectiveness would require stable genotypes to be tested for more than a year. Also preliminary testing of large populations in high-productivity environment only, would not maximise gain from selection in low-productivity zones. But the most productive genotypes in both zones can be identified through concomitant selection for yield in high-productivity environments and for harvest index in low-productivity conditions. RESUME Une interaction significative du génotype avec les écartements de semis, peut être due à des changements de classement des lignées. Elle peut ainsi doubler les ressources nécessaires pour identifier les meilleurs génotypes. Cette étude avait pour but d'estimer l'importance de cette interaction et ses effets sur la sélection et l'évaluation de variétés de niébé (Vigna unguiculata L. Walp). Dix lignées ont été évaluées avec les écartements de semis 50 x 50 et 50 x 25 cm, pendant deux années, dans deux localités. Ces écartements et leur interaction avec le génotype n'ont eu aucun effet significatif sur le rendement en graines et l'indice de récolte. La sélection dans les densités faibles serait alors efficace, pour identifier des génotypes supérieurs destinés aux écartements espacés ou serrés. L'interaction du génotype avec le milieu et les écartements étant significatif, l'efficacité de cette sélection s'appliquerait alors à des génotypes relativement stables, pouvant être évalués plus d'une fois. Aussi, des essais dans des zones favorables seulement, ne sauraient maximiser les gains de sélection pour les environnements défavorables. Cependant, la sélection concomitante pour le rendement en milieu favorable et pour l'indice de récolte en environnements défavorables, peut identifier les génotypes les plus productifs dans les deux zones. (African Crop Science Journal 2001 9(2): 359-368

Heritability estimates, genetic correlation, and identification of RAPD markers linked to seedling vigor and associated agronomic traits in sorghum

Seedling vigor in sorghum (Sorghum bicolor (L.) Moench), is important for improving stand establishment. These studies were conducted to investigate the heritability of the difference in seedling vigor observed between SRN39 and Shanqui red, to assess the genetic relationships of seedling vigor with field performance and phenolic compounds concentrations, and to identify QTLs associated with these characters. One hundred recombinant inbred lines and their parents were evaluated for seedling vigor, crop performance and phenolic compounds concentrations. Percent seed germination at 12\sp\circC and at 22\sp\circC, seedling emergence, seedling height and shoot dry weight were determined under controlled environments. Significant genetic correlation between different estimates of seedling vigor were observed. Germination at 22\sp\circC, emergence, seedling vigor scores, and the rate of seedling dry matter accumulation were significantly correlated with grain yield. High phenolic concentrations were associated with vigorous seedlings, high percent germination at 22\sp\circC, high emergence, and taller seedlings. Only total phenols were significantly associated with grain yield. Lines with a red coleoptile tended to be more vigorous and more productive than lines with a green coleoptile. RAPD markers on linkage groups D and F were significantly associated with seedling vigor scores. Germination at low and at optimum temperatures were mostly under different genetic control. The marker analysis showed that the visual scoring system used was effective in integrating germination, emergence, and seedling height. It was concluded that Shanqui red could be a valuable parent for the development of early maturing varieties that have improved stand establishment, and adapted to environments where low temperatures at planting in spring and early frost in the fall prevail. The identification of markers associated with seedling vigor and field performance should make breeding for the improvement of these traits more efficient, by minimizing the amount of genotype by environment interaction effect