Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity

Implantation de filtres digitaux récursifs à deux dimensions

Les effets de la précision limitée sont considérés pour les filtres digitaux récursifs à deux dimensions. Des erreurs sont introduites dans la quantification de l'entrée, dans les coefficients et dans l'évaluation des multiplications des implantations de filtres. Des modèles de filtres à longueur de registres fini sont développés et différentes formes de réalisation sont montrées. Une approche statistique est adoptée, ce qui permet de calculer la distribution d'erreurs à la sortie de filtres. L'arrondissement et la coupure sont comparés comme méthodes de quantification. Différentes formes d'arithmétique à point fixe sont considérées et quelques examples sont donnés

Indol-butyric acid levels on cashew cloning by air-layering process Níveis de ácido indolbutírico na clonagem do cajueiro pelo processo de mergulhia aérea

A study was conducted to determine the possibility of cashew (Anacardium occidentale) cloning by air-layering and influence of IBA (indol-butyric acid) on this process. It was adopted a completely randomized design with 4 treatments, 10 air layers each and 4 replications, reaching 160 air layers. The IBA levels on the treatments were, as follow: 0, 1000, 3000 and 5000 mg.kg-1. It was evaluated: survival, callus and rooting percentage, average number and length of roots. The highest survival rate (67.5%) was registered with no growth regulator and IBA at 1000 mg.kg-1, while the best rooting percentage (82%) referred to 1000 mg.kg-1. In spite of average number and length of roots, the highest results were observed with IBA at 5000 mg.kg-1. IBA concentrations had no influence on cashew air-layering formation.<br>Um estudo foi conduzido com a finalidade de determinar a possibilidade de clonagem do cajueiro (Anacardium occidentale) por alporquia e a influência do AIB (ácido indolbutírico) nesse processo. Adotou-se delineamento experimental inteiramente casualizado, com 4 tratamentos, 10 alporques por parcela, repetidos por 4 vezes, num total de 160 alporques. Os tratamentos constaram das concentrações de AIB: 0 (testemunha), 1.000, 3.000 e 5.000 mg.kg-1. Foram avaliadas as percentagens de sobrevivência, calejamento e enraizamento, bem como número e comprimento médio de raízes. A maior percentagem de sobrevivência (67,5%) foi observada para a testemunha e concentração de 1.000 mg.kg-1, enquanto a melhor percentagem de enraizamento (82%) foi relacionada com o nível de 1.000 mg.kg-1. Para o número e comprimento médio de raízes, os melhores resultados foram concernentes à dose de 5.000 mg.kg-1. Não houve influência do AIB na clonagem do cajueiro por alporquia

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts

Micrografting of Protea cynaroides

The inability to induce rooting of in vitro-established Protea cynaroides microshoots has prevented the production of complete plantlets. A successful shoot-tip micrografting technique was developed using in vitro-germinated P. cynaroides seedlings as rootstocks and axenic microshoots established from pot plants as microscions. Thirty-day old seedlings, germinated on growth-regulator-free, half-strength Murashige and Skoog medium, were decapitated and a vertical incision made from the top end. The bottom ends of microshoots established on modified Murashige and Skoog medium were cut into a wedge (‘V’) shape, and placed into the incision. The micrografted explants were cultured in a growth chamber with the temperature adjusted to 25 ± 2°C, with a 12-h photoperiod. Best results were obtained by placing the microscions directly onto the rootstock without any pre-treatments. Dipping the explants in anti-oxidant solution or placing a layer of medium around the graft area led to the blackening of the microscion. Abbreviations EDTA Ethylenediaminetetraacetate - BAP 6-Benzylaminopurine - GA3 Gibberellic acid - PAR Photosynthetic active radiatio

Micropropagação de Cabralea canjerana Micropropagation of Cabralea canjerana

A Cabralea canjerana (Vell.) Mart. (Meliaceae) (canjarana) é uma espécie arbórea nativa brasileira importante para fornecimento de madeira de boa qualidade. As sementes desta espécie não podem ser armazenadas por muito tempo e, por tanto, existe a necessidade do desenvolvimento de técnicas alternativas de propagação como a micropropagação. Neste trabalho, foram realizados experimentos de multiplicação utilizando segmentos nodais, retirados de plantas germinadas in vitro. Os segmentos foram inoculados em meio de cultura MS ou WPM, adicionado de 6-benzilaminopurina (BAP) e, ou, 2-isopenteniladenina (2-iP) nas concentrações de 2,5 ou 5 &micro;M. Microestacas de rebrotas foram colocadas em meio de cultura MS/2, com a metade da concentração dos sais do meio MS, adicionado de ácido indol 3-butírico (AIB) (0, 2,5 e 5 &micro;M). Após sete dias, foram transferidas para meio MS/2 sem auxina e na luz. Na fase de multiplicação, o meio de cultura MS foi mais adequado que o meio WPM. O segmento nodal, em presença de 2,5 &micro;M de BAP, propiciou um dos melhores resultados, com uma taxa de multiplicação de 1,77 por mês, em meio de cultura MS. O enraizamento das microestacas oriundas de rebrotas foi de 87,5% em presença de 5 &micro;M de AIB durante sete dias. A aclimatização foi realizada em casa de vegetação e proporcionou 90% de sobrevivência das mudas após 30 dias. A micropropagação da canjarana a partir de segmentos nodais de mudas cultivadas in vitro é viável para a multiplicação dessa espécie.<br>Cabralea canjerana (Vell.) Mart. (Meliaceae) ("canjarana") is a native tree of economic importance in Brazil. The storage of seeds is of short duration and it is therefore necessary to establish a protocol for micropropagation of this species. In this work, multiplication experiments were carried out using nodal segments, excised from in vitro germinated plants. The segments were inoculated in MS or WPM culture medium, supplemented with 6-benzylaminopurine (BAP) and/or 2-isopentenyladenine (2-iP) at 2.5 or 5 &micro;M. Micro-cuttings were taken from new shoots developed from the seeds and used in a rooting experiment using a culture medium with half-strength MS medium (MS/2) supplemented with indolbutyric acid (IBA) (0, 2.5 and 5 &micro;M). After 7 days in this medium, they were transferred to MS/2 medium without auxin under light. During the multiplication phase, the MS culture medium was more suitable for the multiplication of C. canjerana than WPM medium. The nodal segments cultured in the presence of 2.5 &micro;M BAP showed the best result, with a multiplication rate of 1.77 per month on MS medium. The rooting of the microcuttings was 87.5% when they were kept in the presence of 5 &micro;M IBA for 7 days. An acclimatization rate of 90% was achieved after 30 days in the greenhouse. In conclusion, the micropropagation of C. canjerana from nodal segments of plantlets is possible for this species

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Abstract Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts