Upland Rice Breeding in Uganda: Initiatives and Progress

Until recently, there was limited research on breeding upland rice varieties. Moreover, there is an increasing expansion of rice production from traditional irrigated production areas to rain‐fed environments in the East African region, where drought problem is a serious challenge. To date, several initiatives aimed at increasing rice production have been made. Of the initiatives, promotion of upland rice production has been the most important in Uganda, but yield penalty due to drought continued to be a major drawback. This article traces progress in the upland rice breeding that started with improvement of late maturing varieties that had nonpreferred cooking qualities. Initially, introduced lines were evaluated and released. These varieties are the ‘New Rice for Africa’ (NERICA) that had been generated from interspecific crosses involving Oryza glaberrima and Oryza sativa. Several studies to understand the mode of gene action and modified pedigree breeding approaches for drought tolerance were conducted and used to develop new rice varieties. Up to 11 improved upland rice varieties were released and deployed in the country from 2002 to 2011 as a result of this initiative

PROBING VIBRATIONAL WAVE PACKETS IN ORGANOPHOSHOROUS MOLECULES USING FEMTOSECOND TIME-RESOLVED MASS SPECTROMETRY

Organic phosphates and phosphonates share a basic structure with organophoshorous chemical warfare agents and cellular components such as DNA. To understand ultrafast nuclear dynamics in isolated organic phosphates and phosphonates, Femtosecond Time Resolved Mass Spectrometry (FTRMS) was employed. FTRMS applies the pump-probe technique with mass spectrometric detection. In our experiment an ionizing $10^{14}$ W cm$^{-2}$, 1500 nm, 18 fs pump and a non-ionizing $10^{13}$ W cm$^{-2}$, 800 nm, 25 fs probe pulse were used. Experiments were performed on four related compounds: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), diisopropyl methylphosphonate (DIMP) and trimethyl phosphate (TMP). The yields of parent molecular ions generated by the pump pulse exhibited ultrafast oscillations with the period depending on the parent molecule. These oscillations indicate the presence of a vibrational wave packet that is excited upon ionization. In DMMP, a well resolved peak of 45 fs ($732\pm28$ cm$^{-1}$) was observed with a weak feature at 610-650 cm$^{-1}$, while DIMP exhibits bimodal oscillation with frequencies of $554\pm28$ and 670-720 cm$^{-1}$. Oscillations for DEMP were barely visible due to rapid decay. The high- and low- frequency oscillations in DMMP and DIMP were assigned to coherent excitation of O-P-O bend and P-C stretching respectively based on DFT calculations. Bimodal oscillations at 770 and 880 cm$^{-1}$ in TMP were also observed and are tentatively assigned to the symmetric and asymmetric P-O stretching modes. These results suggest that this group of compounds exhibits similar coherent vibrational excitation upon ionization. These results may have applications to development of new organophosphorous chemical warfare agent detection and destruction techniques based on the coherent control and may point to reaction pathways in organophosphorous compounds of biological relevance

Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems

Funding: This research was funded by the Generation Challenge Program (GCP) project G3008.06, “Targeting Drought-Avoidance Root Traits to Enhance Rice Productivity under Water-Limited Environments". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Interplot and intraplot border effects on maize genotypes under two levels of moisture availability

The performance of three maize (Zea mays L.) hybrids, grown under two irrigation levels, was used to investigate the effects of soil moisture competition between adjacent plots, the transmission of these effects into multi-row adjacent plots and types of multi-row plots and plot borders most effective in shielding from these interplot competition effects. On the basis of grain yield, competition effects intended to the second rows of five-row plots necessitating more than five-row plots to accurately evaluate the full transmission of interplot competition effects into adjacent plots. Evaluation of genotypes in one-row plots all with the same common border row genotype to make them three-row plots would be more suitable for evaluation of relative competitiveness for soil moisture under soil moisture stress conditions compared to no border rows or border rows of the same genotype being evaluated

2015 Africa-wide Breeding Task Force Trials for Rainfed Upland

In 2010, the Africa-wide Rice Breeding Task Force was launched by AfricaRice involving National Agricultural Research System (NARS) from about 30 countries. The objectives of the network are to evaluate the stability of traits incorporated in breeding processes and to identify varieties best fit to growth conditions in target regions and to markets. The Task Force also accumulates data on performance of new elite lines, thereby facilitating varietal release procedures. Furthermore, by exposing breeders from NARS and farmers to these elite lines during the testing phase, dissemination will be facilitated. The activities conducted by the Task Force consists of a series of consecutive trials. Promising breeding lines developed by AfricaRice or by national and international partners, such as IRRI, CIAT and the NARS are nominated for evaluation in one or several rice cultivation environments: rainfed lowland, irrigated lowland, rainfed upland, high elevation and mangrove. All nominated lines should be fixed and accompanied by supporting data on traits incorporated during the breeding process and with information on yield performance. These characteristics are checked at AfricaRice before incorporation into the network. The first phase (MET, Multi-Environment Testing) consists of an initial evaluation of about 100 lines selected from the nominated lines. Each national partner evaluates these lines at sites in his/her country. Such sites may be at an experimental station under optimal management to evaluate yield potential, or may be ‘hot spots’ to check the performance of the nominations in a stressed growth environment. Trials are replicated three times and include at least a common and a local check. The second phase (PET,Participatory Evaluation Trial) serves to evaluate and confirm the performance of the selected lines. These lines are cultivated using the same experimental design with 3 replications. An important feature of PET is that farmer and other stakeholders such as miller and traders are invited to participate in varietal selection and their opinion on the performance of all entries (i.e. participatory varietal selection, PVS) collected. Based on the data collected, observations by the breeders and the opinion of stakeholder groups, NARS partners select up to 10 lines. Further, NARS evaluated these lines in at least three sites per country and during one or more growing seasons, depending on varietal release requirements. All stakeholders are again invited to get acquainted with the new lines and voice their opinion to help select lines for further advancement. Among the 10 lines, farmers are invited to select three lines and cultivate these in their own fields, together with a common check and their own variety

The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.): Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. sativa and Ecological Adaptation

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits—possibly reflecting ecological adaptation to different growing environments

Introgression of Two Drought QTLs into FUNAABOR-2 Early Generation Backcross Progenies Under Drought Stress at Reproductive Stage

FUNAABOR-2 is a popular Ofada rice variety grown in a large area under rainfed upland condition across western states of Nigeria. We used the combination of phenotypic and marker-assisted selection (MAS) to improve grain yield of FUNAABOR-2 under drought stress (DS) at the reproductive stage via introgression of two drought quantitative trait loci (QTLs), qDTY12.1 and qDTY2.3. Foreground selection was carried out using peak markers RM511 and RM250, associated with qDTY12.1 and qDTY2.3, respectively, followed by recombinant selection with RM28099 and RM1261 distally flanking qDTY12.1. Furthermore, BC1F2-derived introgressed lines and their parents were evaluated under DS and non-stress (NS) conditions during the 2015–2016 dry season. Overall reduction of grain yield under DS compared to NS was recorded. Introgressed lines with qDTY12.1 and qDTY2.3 combinations showed higher yield potential compared to lines with single or no QTL under DS, indicating significant positive interactions between the two QTLs under the FUNAABOR-2 genetic background. Pyramiding of qDTY12.1 and qDTY2.3 in the FUNAABOR-2 genetic background led to higher grain yield production under DS and NS. Keywords: drought, foreground selection, introgressed line, peak marker, yield potential, rice, quantitative trait locu

Biplots for A) grain yield, B) root dry weight, C) maximum root depth, and D) % deep roots.

<p>Data previously reported by Henry et al (2011), Gowda et al (2012), and Shrestha et al (2013) were used to calculate some of the results shown in this figure.</p

The OryzaSNP germplasm set was phenotyped with a range of root-screening techniques.

<p>A) rhizotron (Ab09CR: Univ Aberdeen), B) penetration of nonwoven fabric (Ab09CNWNW: Univ Aberdeen), C) monoliths from line source sprinkler (Na10 and Na11; Nagoya Univ), D) soil-filled cylinders (Ba10C; Barwale Foundation, and CS09C; Charles Sturt Univ), E) hydroponics (Ab09CH: Univ Aberdeen), F) monoliths in the field (IR08FL and IR09dFL; IRRI), G) lysimeters (IR08C; IRRI, IC09C; ICRISAT), and (H) in the field by excavation (TN10F, TN11F; Tamil Nadu Agric. Univ).</p

A genomic region on chromosome 1 (39.7–40.7 Mb) was identified as a hot spot in which root dry weight, percent deep roots, and yield aligned.

<p>Colors indicate each experiment from which the phenotypic data and introgression regions were correlated. Experiments from which introgression regions fell within the hot spot are identified in the legend.</p