Planting material : what strategy for planters ? : DxP seed is not only DxP seed

For a tropical plant, the oil palm commodity chain includes the peculiarity of possessing a major seed production sector for reasons that are primarily genetic. Planters are always concerned about the reliability and value of the material they plant. Most oil palm plantations (around 70%) belong to large agroindustrial enterprises, but family smallholdings are also developing strongly and are in the majority in numerous countries. However, access to seeds and to information on seeds is not organized in the same way for agro-industries as for smallholders, especially if the latter are in isolated locations. In fact, it is difficult to organize seed distribution to smallholders, and very often they will depend on agro-industry strategy or middlemen networks for their own plantation. Another peculiarity of the oil palm seed market is, despite state or public organization attempts to organize the market, the virtual total absence of guarantees for buyers. It is difficult, if not impossible, to evaluate the quality of the research conducted by breeders. Have commercial seeds, based on scientific criteria, such as yield components, resistance to diseases, to drought, to altitude, to low temperatures, been really developed on these criteria with well-defined and adapted experimental designs? In addition, the seed production strategies, necessary for transferring genetic progress observed in research stations into the commercial seeds, are not all reliable. And, last but not least, the technical quality of production can lead to a not inconsiderable percentage of weak seeds due to uncontrolled pollen contamination. The only guarantee today comes from the relationships of confidence established year after year between breeders/distributors and growers. In this respect, the initial strategy for agro-industry is very often to diversify supply sources in order to guarantee their plantations an "average" value. In a second step, these groups almost always aim to become seed producers themselves. To that end, they can either link-up with breeders to acquire production licences, or if they are seeking greater independence they may attempt to procure parent material and become breeders in their own right. In either case, they must take on a major risk of ending up with a planting material that might not perform well, as the different materials available on the market display substantial production differences that can exceed 20%. In such a case, the very future of a major industrial group could be jeopardized. In these fields, research can lead to some proposals: to help public institutions to define a seed certification policy, molecular biology offers some interesting prospects for certifying seed quality (contamination rates and genetic origin), and social science could develop effective communication methods towards planters. (Résumé d'auteur

Identification of Ganoderma disease resistance loci using natural field infection of an oil palm multiparental population

Multi-parental populations are promising tools for identifying quantitative disease resistance loci. Stem rot caused by Ganoderma boninense is a major threat to palm oil production, with yield losses of up to 80% prompting premature replantation of palms. There is evidence of genetic resistance sources, but the genetic architecture of Ganoderma resistance has not yet been investigated. This study aimed to identify Ganoderma resistance loci using an oil palm multi-parental population derived from nine major founders of ongoing breeding programs. A total of 1200 palm trees of the multi-parental population was planted in plots naturally infected by Ganoderma, and their health status was assessed biannually over 25 yr. The data were treated as survival data, and modeled using the Cox regression model, including a spatial effect to take the spatial component in the spread of Ganoderma into account. Based on the genotypes of 757 palm trees out of the 1200 planted, and on pedigree information, resistance loci were identified using a random effect with identity-by-descent kinship matrices as covariance matrices in the Cox model. Four Ganoderma resistance loci were identified, two controlling the occurrence of the first Ganoderma symptoms, and two the death of palm trees, while favorable haplotypes were identified among a major gene pool for ongoing breeding programs. This study implemented an efficient and flexible QTL mapping approach, and generated unique valuable information for the selection of oil palm varieties resistant to Ganoderma disease

Advances in oil palm genomic selection

More efficient methods are required to breed oil palm (Elaeis guineensis Jacq.) for yield maximization, in order to meet the increased demand for palm oil while limiting environmental impacts. Today, genomic selection (GS) appears to be a disruptive improvement that can speed up breeding schemes by avoiding field trials in some cycles and increase selection intensity by the application of selection to a larger number of candidates than with the current methods. Oil palm is becoming a model species for GS, as it is one of the perennial crops with the largest number of published articles. GS was evaluated in oil palm for the prediction of parental general combining abilities and performances of hybrid crosses and clones. In all cases, GS accuracies high enough to allow selection were obtained for some traits. Best accuracies were obtained when training and validation populations were highly related, such as full-sibs or progenies. Array-based SNPs and GBS-derived SNPs allowed cost effective GS predictions, with densities of a few thousand markers being sufficient. Widely used statistical methods of GS predictions GBLUP and rrBLUP appeared efficient, and could be optimized by SNP filtering methods. Approaches to limit the increase in the rate of inbreeding associated with GS were identified. Evaluations of the annual genetic progress showed that GS should bring it to an unprecedented level. Further studies remain required for the optimal application of GS in oil palm. They should focus in particular on the optimization of training populations, the improvement of prediction models, the variation of GS accuracy between families, the use of multi-omics data (transcriptomics, proteomics, etc.), the modeling of G × E interactions and inter-specific selection

Congrès international sur le palmier à huile organisé par le PORIM (PIPOC 1999)

En amélioration des plantes, la recherche de matériels à forts rendements se poursuit. Cela passe par la sélection classique en identifiant de nouvelles populations, en utilisant les ressources génétiques pour améliorer les défauts des populations actuelles. Cela passe aussi par la mise au point des clones de palmier à huile. Bien que l'on soit toujours confronté au problème de l'anomalie florale, les études sur la valeur des clones par rapport au matériel sexué confirment l'intérêt des clones. La biologie moléculaire est aussi utilisée dans les études sur le palmier à huile pour préparer la sélection assistée par marqueurs, mais aussi pour identifier les causes de l'anomalie florale des clones. En agronomie et protection des cultures, de nombreuses études présentées mettent en évidence des carences de management des plantations. En effet, de nombreuses interventions traitent de problèmes déjà connus et étudiés par le passé. Cependant, il est intéressant de noter l'émergence de nouvelles techniques (systèmes d'information géographique) et la meilleure prise en compte de l'impact écologique ainsi que les interactions avec les réserves naturelle

Potential of genomic selection in perennial crops: preliminary results in the context of Eucalyptus and oil palm breeding : P-180

The methodology of selection in plant breeding has markedly evolved with the advent of high throughput molecular technology, the increasingly reasonable cost of genotyping, and the implementation of genomic selection (GS). For perennial crops, the potential of GS is high and gives the opportunity to shorten the breeding cycle by selecting at the juvenile stage using marker information. Here we present preliminary results of GS experiments for two perennials crop, Eucalyptus and oil palm, that play an important economical role in tropical regions. In the case of Eucalyptus, a simulation study was developed to test the efficiency of GS in the frame of a recurrent selection scheme for clone production over four breeding cycles. Scenarios crossing broad sense heritabilities (H²=0.6 and 0.1), dominance to additive variance ratios (R=0.1; 0.5 and 1) and training population structure were compared using Bayesian LASSO method. Models including dominance effects are all the more relevant when the R ratio and the training population size are high. The genetic gain per unit time with GS was 1.5 to 3 times higher than with phenotypic selection at mature stage for breeding and clone populations. For oil palm, we implemented a cross-validation approach with 111 individuals of the last generation of a key breeding population, evaluated through progeny tests including 40,000 individuals and genotyped with 140 microsatellites. The accuracy of GS increased when increasing the training population size and reached 0.6-0.7, according to the trait, with a 3:1 ratio for training and validation populations respectively. The small effective population size detected in this breeding population explains the good GS performance even with a limited panel of markers. Our studies based on two perennials crops presenting different biological patterns and different breeding contexts suggest very promising results of GS for long rotation plant species. (Texte integral

Agrigenomics in the breeder's toolbox: latest advances towards an optimal implementation of genomic selection in oil palm

PalmElit implements the genetic improvement and marketing programs for CIRAD® oil palm seeds. The commercial seeds embody 80 years of genetic improvement work undertaken by IRHO, CIRAD and PalmElit in conjunction with several partners of excellence located on each of the continents where oil palm is grown. An increase of more than 60% in oil yields was achieved since 1960. This result illustrates the efficiency of the recurrent reciprocal selection (RRS) underlying the conducted breeding program. So far, assessment of parental breeding values has largely relied on progeny testing, which is an efficient but time- and money-consuming step within the RRS scheme. With the recent development of oil palm genomic resources, genomic selection (GS) appears as an attractive strategy to increase the efficiency of oil palm breeding programs. On a theoretical point of view, GS has the potential to increase the rate of genetic gain by shortening the breeding cycle and/or increasing the selection intensity. PalmElit, together with its research partner CIRAD, has been leading research for nearly 10 years in order to develop and assess the implementation of GS in oil palm breeding. Some of the key achievements have been shared with the scientific community since 2015 (Cros et al., 2015a, 2015b, 2017a; Marchal et al., 2016) which corroborate the potential of GS in terms of increased genetic gain. Further research is still ongoing to answer the simple -but critical- question: what is the optimal use of GS in terms of genetic gain vs time- and cost-efficiency? In this paper, following a brief review on the GS history and key concepts, we present our latest results which address critical aspects such as prediction accuracy and optimal use of GS within breeding schemes. We extend and discuss our conclusions in light of the literature available in oil palm and other crop species. Finally, we summarize the perspectives and challenges for successful implementation of GS in oil palm

Intensification of oil palm (Elaeis guineensis Jacq.) plantation efficiency through planting material: New results and developments

Indonesia recently pledged to become a major global food producer by boosting the production of food commodities. Palm oil is one of the 10 strategic and key commodities that are part of the government's 2009 - 2014 road-map for food development. Domestic palm oil producers are being encouraged to expand their plantations from the current 7.9 million hectares in 2009 to 9.7 million hectares by 2015. Indonesia goal is to boost CPO production to 36.6 million tonnes per year (Maulia, 2010). The apparent stagnation of long term palm oil yield trends in the dominant producing countries, such as Malaysia and Indonesia, is considered a vital concern for the oil palm industry and this new agenda makes the intensification of plantation efficiency more necessary, in the context of sustainable palm oil production. Planting material quality has been recognised as a key input for oil palm sustainability. Where the technical efficiency of growers in all the best management practices (BMPs) is optimum, yield enhancement through the improvement of planting materials will remain the main source of economic progress or sustainability (Baskett et al., 2008). The most recent results from the PT Socfindo Aek Loba Timur Breeding project and their transfer to the commercial plantations accompanied by a stringent selection of the best parental families with a 10 tonnes Total Oil/ha/year target, are presented. New developments in the PT Socfindo Research & Development programmes such as the implementation of a new selection cycle evaluating the whole parental collection and a new seed garden at the Aek Loba Estate, the development of an early test as a key input in breeding for Ganoderma resistance, or the medium-term search for high-yielding planting material less demanding in fertilizer input are also discussed. (Résumé d'auteur