Site Specific Nutrient Management for Maize on Ultisols Lampung

Site Specific Nutrient Management  for Maize on Ultisols Lampung (A M Murni, JM Pasuquin, and C Witt): Lampung is the third major maize producing province in Indonesia after East Java and Central Java. In Lampung maize is cultivated mainly in upland areas with ultisols and only some cultivated on paddy field as a secondary crop in the dry season. The average maize yield in Lampung is still 3.4 Mg ha-1 bellow yield potential of 7-10 Mg ha-1. To increase the productivity of maize through site-specific nutrient management (SSNM), on-farm trials were conducted in five locations in Lampung i.e. four locations in Central Lampung District (Sidowaras, Binjai Ngagung, Watu Agung and Balai Rejo) and one location in South Lampung District (Trimulyo, Tegineneng Sub District) during the 2004/2005, 2005/2006 and 2006/2007 rainy seasons. The experimental setup followed a standard protocol at all sites and included nutrient omission plots (PK, NK, NP) to estimate indigenous nutrient supplies, an NPK plot to measure yield response to fertilizer application, and a farmers’ fertilizer practice (FFP) plot in each farmer’s field. An SSNM treatment plot was included in the second and third seasons. Each of the above treatments was paralleled by a plot with improved crop management practice (ICM), i.e. higher planting density, addition of lime, and addition of magnesium. Results showed that yield response to fertilizer N, P and K application in these sites were: N = 2.3-4.1 Mg ha-1; P = 0.6-2.0 Mg ha-1; K = 0.3-2.4 Mg ha-1. Attainable yield in the three seasons on average ranged from 7.6 Mg ha-1 to 10.6 Mg ha-1. Yield in the SSNM treatment (with or without ICM) was significantly higher than the FFP indicating great opportunities for farmers to increase productivity and profitability with improved nutrient and crop management.

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Background:Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity andgreatly affect rice yield and quality. To improve rice production, understanding the genetic and molecularresistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is aneffective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the geneticrelationship between them in a genetically diverse population.Results:A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW),shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe orSZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a,qSdw3b,qSdw12andqSFe5/qSZn5) were detected in the same genomic regions under the two stress conditionsand 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses.Conclusion:Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidategenes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information forfuture functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assistedselection or designed QTL pyramiding

Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility

Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at P<1 × 10−5 (33 at P<1 × 10−4) were related to sterility effects of heat, cold, cold acclimation, or unexplained causes (baseline sterility). Nine annotated genes were found on average within the 50% linkage disequilibrium (LD) region. Among them, one to five plausible candidate genes per QTL were identified based on known expression profiles (organ, stage, stress factors) and function. Meiosis-, development- and flowering-related genes were frequent, as well a stress signaling kinases and transcription factors. Putative epigenetic factors such as DNA methylases or histone-related genes were frequent in cold-acclimation QTLs, and positive-effect alleles were frequent in cold-tolerant highland rice from Madagascar. The results indicate that epigenetic control of acclimation may be important in indica rice genotypes adapted to cool environments. (Résumé d'auteur

Site Specific Nutrient Management for Maize on Ultisols Lampung

Lampung is the third major maize producing province in Indonesia after East Java and Central Java. In Lampungmaize is cultivated mainly in upland areas with ultisols and only some cultivated on paddy field as a secondary cropin the dry season. The average maize yield in Lampung is still 3.4 Mg ha-1 bellow yield potential of 7 - 10 Mg ha-1. Toincrease the productivity of maize through site-specific nutrient management (SSNM), on-farm trials were conductedin five locations in Lampung i.e. four locations in Central Lampung District (Sidowaras, Binjai Ngagung, Watu Agungand Balai Rejo) and one location in South Lampung District (Trimulyo, Tegineneng Sub District) during the 2004/2005,2005/2006 and 2006/2007 rainy seasons. The experimental setup followed a standard protocol at all sites and includednutrient omission plots (PK, NK, NP) to estimate indigenous nutrient supplies, an NPK plot to measure yield responseto fertilizer application, and a farmers’ fertilizer practice (FFP) plot in each farmer’s field. An SSNM treatment plot wasincluded in the second and third seasons. Each of the above treatments was paralleled by a plot with improved cropmanagement practice (ICM), i.e. higher planting density, addition of lime, and addition of magnesium. Results showedthat yield response to fertilizer N, P and K application in these sites were: N = 2.3 - 4.1 Mg ha-1; P = 0.6 - 2.0 Mg ha-1;K = 0.3-2.4 Mg ha-1. Attainable yield in the three seasons on average ranged from 7.6 Mg ha-1 to 10.6 Mg ha-1. Yield inthe SSNM treatment (with or without ICM) was significantly higher than the FFP indicating great opportunities forfarmers to increase productivity and profitability with improved nutrient and crop managemen

Additional file 5: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Significant SNPs associated with measured traits in Fe experiment. (XLSX 34 kb

Additional file 3: of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

ANOVA results for the measured traits under zinc toxicity for 211 indica accessions. (DOCX 26 kb

Additional file 1: Figure S1. of QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

PCA 3D plot of the first three principal components (PC) in 222 accessions (a) and 211 accessions (b); Table S1. List of indica accessions used in the present study. (DOCX 201 kb