Molecular evidence that Meloidogyne hapla, M. chitwoodi, and M. fallax are distinct biological entities

Six isolats de #Meloidogyne hapla - quatre de la race A et deux de la race B -, huit de #M. chitwoodi et cinq de #M. fallax ont été soumis à une électrophorèse bidimensionnelle sur gel (2-DGE) afin d'étudier la similarité intraspécifique des isolats appartenant à chacune des trois espèces, ceci basé sur les protéines solubles totales. Pour chaque isolat, deux échantillons distincts de 50 jeunes femelles gravides ont été extraits des racines. Chaque échantillon a été utilisé pour réaliser un mini-gel bidimensionnel. Les mini-DGE révèlent une moyenne de 400 spots protéiniques par gel. A l'intérieur de chaque espèce, tous les gels ont été comparés entre eux pour identifier deux types de spot polymorphiques : les variants liés au point isoélectrique (IP), et les variants présents-absents (PA). Ont été observés parmi les isolats de #M. hapla, treize variants PA et neuf variants IP, pour #M. chitwoodi huit PA et aucun IP et pour #M. fallax deux PA et aucun IP, ceci correspondant à un polymorphisme de 5,0, 2,2 et 0,6% pour, respectivement, chacune des trois espèces. Ces valeurs impliquent une très faible variabilité intra-spécifique. Elles confirment également que ces espèces constituent des entités biologiques bien délimitées car la similarité entre ces espèces est significativement plus faible qu'entre isolats de la même espèce. L'utilisation de l'UPGMA pour les neuf variants IP de #M. hapla$ conduit à un dendrogramme de similarité séparant nettement les isolats de la race A de ceux de la race B. (Résumé d'auteur

Genetic variation among parthenogenetic Meloidogyne species revealed by AFLPs and 2D-protein electrophoresis contrasted to morphology

Des isolats appartenant aux espèces parthénogénétiques améiotiques #Meloidogyne arenaria, #M. hapla race B, #M. incognita, #M. javanica et parthénogénéiques méiotiques #M. chitwoodi, #M. fallax, #M. hapla race A, #M. naasi ont été comparés quant à leurs protéines totales solubles - par électrophorèse sur gel en deux dimensions (2-DGE) -, leur ADN génomique total - par AFLP - et leurs caractères morphologiques - par mensurations directes et données provenant de la littérature. Ces données ont été transformées en coefficients de similarité en utilisant le coefficient Dice basé sur plus de 100 spots protéiniques, 192 fragments d'AFLP et 21 caractères morphologiques. Les dendogrammes, établis suivant la méthode UPGMA basés sur les données fournies par les protéines et l'ADN sont congruents. Le groupement des races A et B de #M. hapla montre une similarité élevée, les trois espèces tropicales #M. incognita, M. javanica et #M. arenaria forment un autre groupe et les espèces spécialisées envers les graminées, #M. naasi, #M. chitwoodi; #M. fallax, sont distantes des autres, les deux dernières montrant une similarité élevée. Le dendogramme basé sur les données morphologiques diffère de ceux basés sur les données moléculaires, notamment pour #M. incognita et #M. naasi$. Il est discuté de cette non correspondance entre données provenant des protéines et de l'ADN, d'une part, et données morphologiques, d'autre part. (Résumé d'auteur

A Pilot Study on the Prevalence of Micronutrient Imbalances in a Dutch General Population Cohort and the Effects of a Digital Lifestyle Program

Maintaining an adequate micronutrient status can be achieved by following a complete, diverse diet. Yet, food trends in Western countries show suboptimal consumption of healthy nutrients. In this study, we explored the prevalence of vitamin and mineral imbalances in a general population cohort of Dutch adults and evaluated the effect of a digital lifestyle program on the nutritional status and nutrition health behaviors of these individuals. A micronutrient panel was measured in 348 participants, alongside a dietary assessment. One hundred users subsequently underwent a remeasurement. We identified at least one nutritional imbalance in 301 individuals (86.5%). A total of 80% improved and normalized B6, 67% improved folate, 70% improved B12, and 86% improved vitamin D. Iron abnormalities were corrected in 75% of the participants. In conclusion, this study found that micronutrient deficiencies of easily obtainable vitamins through diet or supplementation such as B vitamins and vitamin D were more prevalent than expected in a Dutch population. This can partly be explained by insufficient consumption of food groups rich in B vitamins. Our preliminary results in those remeasured after a digitally enabled lifestyle intervention show these imbalances can be corrected with adequate behavioral support complemented with supplementation where needed

Genetic divergence and molecular characterization of sorghum hybrids and their parents for reaction to Atherigona soccata (Rondani).

Simple sequence repeat (SSR) markers linked to quantitative trait loci (QTL) associated with resistance to sorghum shoot fly, Atherigona soccata resistance were used to characterize the genetic and phenotypic diversity of 12 cytoplasmic male-sterile (CMS) and maintainers, 12 restorer lines, and 144 F1 hybrids. The genetic diversity was quite high among the shoot fly-susceptible parents and the hybrids based on them, as indicated by high polymorphic information content (PIC) values, while limited genetic diversity was observed among shoot fly-resistant lines. The phenotypic and genotypic dissimilarity analysis indicated that the shoot fly-resistant and -susceptible parents were 73.2 and 38.5% distinct from each other, and the morphological and genetic distances of certain resistant and susceptible cross combinations was more than their resistant or susceptible parents. Genetic variability among the groups was low (10.8%), but high within groups (89.2%). The genetic and morphological distances suggested that the F1 hybrids were closer to CMS (5 to 12% dissimilar) than the restorer (11 to 87% dissimilar), suggesting that CMS influences the expression of resistance to sorghum shoot fly. The SSR markers can be used to characterize the homologous traits in sorghum germplasm

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discusse

Impact of farmers’ practices and seed systems on the genetic structure of common sorghum varieties in Kenya and Sudan

To understand the effect of different farming systems on the dynamics of diversity of sorghum (Sorghum bicolor (L.) Moench) crop, genetic structure of widely used landraces and modern varieties collected from two contrasting agroecosystems, in eastern Sudan and western Kenya, were analysed with 16 polymorphic microsatellite markers. A total of 1104 accessions, grouped into 46 samples from individual farmers, were genotyped. Cluster analysis of the samples from the two countries displayed contrasting patterns. Most strikingly, differently named landraces from western Kenya formed widely overlapping clusters, indicating weak genetic differentiation, while those from eastern Sudan formed clearly distinguishable groups. Similarly, samples of the modern variety from Sudan displayed high homogeneity, whereas the most common modern variety from western Kenya was very heterogeneous. The high degree of fragmentation of farmlands of western Kenya, coupled with planting of different sorghum varieties in the same fields, increases the likelihood of inter-variety gene flow. This may explain the low genetic differentiation between the differently named landraces and heterogeneity of the modern variety from western Kenya. This study highlights the important role of farmers in shaping the genetic variation of their crops and provides population parameter estimates allowing forecasting of the fate of ‘modern’ germplasm (conventional or genetically modified) when introduced into subsistence farming systems

Opportunities for marker-assisted selection (MAS) to improve the feed quality of crop residues in pearl millet and sorghum

Cereal crop residues (straw, chaff, etc.) are important components of maintenance rations for ruminant livestock in many parts of the world. They are especially important in small-holder crop-livestock production systems in the sub-humid, semi-arid, and arid tropics and subtropics where most of the world's poorest livestock producers and consumers are found. Taking as examples tropically adapted cereals in the crop improvement mandate of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), namely pearl millet [Pennisetum glaucum (L.) R. Br.] and sorghum [Sorghum bicolor (L.) Moench], this paper explores opportunities for using marker-assisted crop breeding methods to improve the quality and quantity of cereal crop residues for use as ruminant livestock feedstuffs. In the case of pearl millet, ICRISAT has been heavily involved with several UK-based collaborating research institutes, in development and initial application of the molecular genetic tools for marker-assisted breeding. We have obtained some useful experience in quantitative trait loci (QTL) mapping and marker-assisted selection (MAS) for stover yield, foliar disease resistance, and in vitro estimates of the nutritive value of various stover fractions for ruminants. In sorghum, ICRISAT has focused on initiating a large-scale high-throughput marker-assisted backcrossing program for the stay-green component of terminal drought tolerance - a trait that is likely to be associated not only with more stable grain and stover yield, but which is also expected to contribute to maintenance of ruminant nutritional value of stover produced under drought stress conditions. Conventional and marker-assisted breeding for foliar disease resistance is recommended for dual-purpose cereal improvement, or indeed for improvement of the nutritional value of residues for any crop in which these are used as feedstuffs for ruminant livestock. Practical problems faced and proposed ways of dealing with these are discussed

Improved hardness results for the guided local Hamiltonian problem

Estimating the ground state energy of a local Hamiltonian is a central problem in quantum chemistry. In order to further investigate its complexity and the potential of quantum algorithms for quantum chemistry, Gharibian and Le Gall (STOC 2022) recently introduced the guided local Hamiltonian problem (GLH), which is a variant of the local Hamiltonian problem where an approximation of a ground state (which is called a guiding state) is given as an additional input. Gharibian and Le Gall showed quantum advantage (more precisely, BQP-completeness) for GLH with 6-local Hamiltonians when the guiding state has fidelity (inverse-polynomially) close to 1/2 with a ground state. In this paper, we optimally improve both the locality and the fidelity parameter: we show that the BQP-completeness persists even with 2-local Hamiltonians, and even when the guiding state has fidelity (inverse-polynomially) close to 1 with a ground state. Moreover, we show that the BQP-completeness also holds for 2-local physically motivated Hamiltonians on a 2D square lattice or a 2D triangular lattice. Beyond the hardness of estimating the ground state energy, we also show BQP-hardness persists when considering estimating energies of excited states of these Hamiltonians instead. Those make further steps towards establishing practical quantum advantage in quantum chemistry