Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections

Direct seeding saves time and labour in the cultivation of rice. However, seedling establishment is often unstable, and yields are lower than in transplanting. Anaerobic germination (AG) is a key trait for improvement of direct seeding of rice. We established a simple and reliable method of evaluating AG in rice breeding. We germinated seeds in distilled water or deoxygenated water and measured coleoptile length several days later; compared the results of each method with survival rate in flooded soil; and used the anoxic water method for QTL analysis and for testing cultivars. Coleoptile elongation in anoxic water and survival rate in flooded soil were significantly correlated (r = 0.879, P < 0.01). A significant QTL, likely to be a major gene (AG1), was found in chromosome segment substitution lines and in a backcrossed F2 population derived from tolerant and sensitive lines. Diverse rice genetic resources were classified into tolerant or sensitive accession groups reflecting their ecotypes. Our study revealed that anoxic water evaluation method saves space and time in a stable environment compared with flooded soil evaluation. It is applicable to QTL analysis and isolation of genes underlying anaerobic germination

Global demand for rice genetic resources

The International Rice Research Institute (IRRI) holds in trust the world's largest collection of rice diversity, with more than 130,000 accessions of cultivated rice and wild species. Between 2012 and 2018, a total of 2174 requests for rice germplasm were received from more than 1000 unique requestors. We documented and analyzed how genebank users made use of germplasm from IRRI. As we address food and nutrition security challenges in a changing context, we are motivated by the need to enhance the conservation, management, and use of rice genetic resources

Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit

Different genes involved in ABA and calcium signaling in leaf tissue of rice NILs and the parent IR64 under different water-deficit treatments. 1: up-regulated; -1: down-regulated; blank: no change in expression; 10: IR77298-14-1-2-B tolerant NIL, i.e., IR77298-14-1-2-B-10; 13: IR77298-14-1-2-B susceptible NIL, i.e., IR77298-14-1-2-B-13; 18: IR77298-5-6-B tolerant NIL, i.e., IR77298-5-6-B-18; 11: IR77298-5-6-B susceptible NIL, i.e., IR77298-5-6-B-11; 0.2 and 0.5 FTSW are severe and mild water-deficit treatments (XLSX 46 kb

Inheritance of traits associated with seed size in groundnut (Arachis hypogaea L.)

Inheritance of groundnut (Arachis hypogaea L.) seed traits particularly seed weight, seed length, seed width and length:width ratio was explored in this study. Six-generation mean analysis was carried with two groundnut crosses and their reciprocals in 2 years. Groundnut genotypes significantly differing in seed sizes were used as parents. Highly significant reciprocal differences were observed for almost all the traits in F1, F2, and BC generations. Additive genetic effects were highly significant and explained majority of the variation in these traits. Results suggest that the seed size traits studied in this study were controlled both by combination of both maternal and nuclear gene effects. All the four seed traits measured were highly correlated suggesting that they could be simultaneously improved. Significance of additive effect in all the four crosses suggests that effective selection for seed size traits could be practiced in early generations. In breeding program for confectionary traits it is essential to include a large-seeded genotype as the female parent to exploit the maternal effects

Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64

The NAC (NAM, ATAF1/2 and CUC2) genes are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. We describe the rice (Oryza sativa) OsNAC genes expression profiles (GEPs) under normal and water-deficit treatments (WDTs). The GEPs of the OsNAC genes were analyzed in 25 tissues covering the entire life cycle of Minghui 63. High expression levels of 17 genes were demonstrated in certain tissues under normal conditions suggesting that these genes may play important roles in specific organs. We determined that 16 genes were differentially expressed under at least 1 phytohormone (NAA, GA3, KT, SA, ABA, and JA) treatment. To investigate the GEPs in the root, leaf, and panicle of three rice genotypes [e.g., 2 near-isogenic lines (NILs) and IR64], we used two NILs from a common genetic combination backcross developed by Aday Selection and IR64. WDTs were applied using the fraction of transpirable soil water at severe, mild, and control conditions. Transcriptomic analysis using a 44K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from the two NILs under both WDTs, and the majority of the OsNAC genes that were activated were in the drought-tolerant IR77298-14-1-2-B-10 line compared with the drought-susceptible IR77298-14-1-2-B-13 or IR64. In IR77298-14-1-2-B-10, seventeen genes were very specific in their expression levels. Approximately 70 % of the genes from subgroups SNAC and NAM/CUC3 were activated in the leaf, but 37 % genes from subgroup SND were inactivated in the root compared with the control under severe stress conditions. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00438-012-0686-8) contains supplementary material, which is available to authorized users

Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity

AbstractIron (Fe) toxicity is recognized as one of the most widely spread soil constraints for rice production especially in West Africa. Oryza glaberrima the cultivated rice species that originated from West Africa is well-adapted to its growing ecologies. The aim of this study was to identify the promising O. glaberrima accessions tolerant to Fe toxicity from the 2106 accessions held at the AfricaRice gene bank. The screenings were conducted over a four-year period and involved evaluating the entries under Fe-toxic field conditions in West Africa, selecting good yielding accessions and repeating the testing with newly selected lines. Three accessions (TOG 7206, TOG 6218-B and TOG 7250-A) were higher yielding than O. sativa checks under stress but with similar yields under control conditions. These accessions yielded over 300g/m2 under both Fe toxicity and control conditions. In conclusion, these materials could be used as donors in breeding programs for developing high yielding rice varieties suited to Fe toxicity affected areas in West Africa

Iron and zinc concentrations in peanut (Arachis hypogaea L.) seeds and their relationship with other nutritional and yield parameters

Biofortification (delivery of micronutrients via micronutrient-dense crops) can be achieved through plant breeding and offers a cost-effective and sustainable approach to fighting micronutrient malnutrition. The present study was conducted to facilitate the initiation of a breeding programme to improve the concentration of iron (Fe) and zinc (Zn) in peanut (Arachis hypogaea L.) seeds. The experiment was conducted with 64 diverse peanut genotypes for 2 years in eight different environments at the International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India to assess the genetic variation for Fe and Zn concentrations in peanut seeds and their heritability and correlations with other traits. Significant differences were observed among the genotypes and environments for Fe (33–68 mg/kg), Zn (44–95 mg/kg), protein (150–310 mg/g) and oil (410–610 mg/g) concentration in seeds and their heritability was high, thus indicating the possibility of improving them through breeding. As seen in other plants, a significant positive association between concentrations of Fe and Zn was observed. Trade-offs between pod yield and Fe and Zn concentrations were not observed and the same was also true for oil content. Besides being high yielding, genotypes ICGV 06099 (57 mg/kg Fe and 81 mg/kg Zn) and ICGV 06040 (56 mg/kg Fe and 80 mg/kg Zn) had stable performance for Fe and Zn concentrations across environments. These are the ideal choices for use as parents in a breeding programme and in developing mapping populations

Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64

The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis