J. R. Witcombe

Farmer Participatory Crop Improvement. I. Varietal Selection and Breeding Methods and Their Impact on Biodiversity

Farmer participatory approaches for the identification or breeding of improved crop cultivars can be usefully categorized into participatory varietal selection (PVS) and participatory plant breeding (PPB). Various PVS and PPB methods are reviewed. PVS is a more rapid and cost-effective way of identifying farmer-preferred cultivars if a suitable choice of cultivars exists. If this is impossible, then the more resource-consuming PPB is required. PPB can use, as parents, cultivars that were identified in successful PVS programmes. Compared with conventional plant breeding, PPB is more likely to produce farmer-acceptable products, particularly for marginal environments. The impact of farmer participatory research on biodiversity is considered. The long-term effect of PVS is to increase biodiversity, but where indigenous variability is high it can also reduce it. PPB has a greater effect on increasing biodiversity although its impact may be limited to smaller areas. PPB can be a dynamic form of in situ genetic conservation.

Breeding for abiotic stresses for sustainable agriculture

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.

Participatory plant breeding is better described as highly client-oriented plant breeding. I. four indicators of client-orientation in plant breeding

SUMMARY In this paper we attempt to remove the dichotomy created by distinguishing between participatory and non-participatory breeding programmes by using the degree of client orientation as the basis for an analysis. Although all breeding programmes are implicitly client-oriented, we examine how participatory approaches explicitly increase the extent of client orientation. We briefly review the history of participatory plant breeding (PPB) and analyse the participatory techniques used at different stages of the breeding programme. In common with several other authors, we find that farmer involvement in selecting in the segregating generations may not be an essential component of PPB. However, in some circumstances such collaboration is required and is the subject of a second paper in this series. The purpose of all the techniques used in PPB programmes is to better meet the needs of clients. Thus, breeding programmes can be differentiated by their extent of client-orientation removing the dichotomy involved with the term participatory. We discuss four techniques in the suite of techniques that have been employed by PPB: identifying the target market or clients; using germplasm that can best meet the needs of target clients; matching the environments of the target clients; and product testing in the target market with target clients. Most attention is paid to the last of these four that is often referred to as participatory varietal selection (PVS) and how it is done varies with circumstances. Rice varieties from a client-oriented breeding programme in Nepal were tested in mother and baby trials in Bangladesh. The rapid acceptance of these varieties by farmers illustrates the power of the participatory trials system and the success of a highly client-oriented breeding approach.

An RFLP-based genetic map of pearl millet (Pennisetum glaucum)

Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F2 population, derived from a single F1 plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.

Mapping quantitative trait loci for downy mildew resistance in pearl millet.

Quantitative trait loci (QTLs) for resistance to pathogen populations of Scelerospora graminicola from India, Nigeria, Niger and Senegal were mapped using a resistant x susceptible pearl millet cross. An RFLP map constructed using F2 plants was used to map QTLs for traits scored on F4 families. QTL analysis was carried out using the interval mapping programme Mapmaker/QTL. Independent inheritance of resistance to pathogen populations from India, Senegal, and populations from Niger and Nigeria was shown. These results demonstrate the existence of differing virulences in the pathogen populations from within Africa and between Africa and India. QTLs of large effect, contributing towards a large porportion of the variation in resistance, were consistently detected in repeated screens. QTLs of smaller and more variable effect were also detected. There was no QTLs that were effective against all four pathogen populations, demonstrating that pathotype-specific resistance is a major mechanism of downy mildew resistance in this cross. For all but one of the QTLs, resistance was inherited from the resistant parent and the inheritance of resistance tended to be the result of dominance or over-dominance. The implications of this research for pearl millet breeding are discussed.

Number of crosses and population size for participatory and classical plant breeding

In the breeding of self-pollinating crops, crossing creates variation upon which selection is exerted. If the value of crosses cannot be predicted then this uncertainty means that many crosses need to be made. However, since there is a limit to the capacity of a breeding programme, more numerous crosses result in each cross having a small population size, fewer progenies in later generations and a lower probability of recovering good genotypes from each cross. Published theory on the optimum number of crosses in a plant breeding programme, for a predominantly self-pollinating crop, usually assumes that all crosses are equal value. This overestimates the number of crosses required. When the optimum size of a population in a favourable cross is considered, theory predicts that very large populations are desirable. The required population size is even larger if linkage of loci controlling different traits is also considered. Hence, in an inbreeding crop, one possible strategy is to select a small number of crosses that are considered favourable and produce large populations from them to increase the probability of recovering superior genotypes. In an out breeding crop, the analogy is a few composites with large population sizes. This low-cross-number strategy is ideally suited to the particular constraints and advantages of participatory plant breeding. Such an approach, although not essential, may still be advantageous in classical breeding. When a breeding programme is based on few crosses, which parents are chosen is crucial and farmer participatory methods are highly effective in narrowing the choice. Modified bulk population breeding methods, and recurrent selection are desirable strategies in the participatory plant breeding of self-pollinating crops when combined with a low-cross-number approach.

Farmer participatory crop improvement. IV. The spread and impact of a rice variety identified by participatory varietal selection

Participatory varietal selection in a development project in western India showed that the rice ( Oryza sativa ) variety Kalinga III was highly preferred by farmers. The spatial diffusion of this variety from three villages (two project and one non-project) was studied. Seed of Kalinga III had spread from the three villages in 1994 to 41 villages by 1996 and is estimated to have reached over 100 widely distributed villages by 1997. Farmer-to-farmer spread was as high from the non-project case study village that received no further seed from the project, possibly because farmers are more likely to spread seed of a new variety to other farmers when they have no assured supply. Project interventions used key villages, informal-sector seed merchants, and Non-Government Organizations in the spread of seed. The project also collaborated with Rajasthan State Agricultural University and Kalinga III has been proposed for release in that state. A financial analysis revealed the very high internal rates of return that are possible from investment in participatory varietal selection.

Analysis of recombination rate in female and male gametogenesis in pearl millet (Pennisetum glaucum) using RFLP markers

Sex as a factor affecting recovered recombination in plant gametes was investigated in pearl millet, Pennisetum glaucum, by using reciprocal three-way crosses [(AxB)xCvCx(A x B)]. The two populations were mapped at 42 loci pre-selected to cover the majority of the genome. No differences in recombination distances were observed at the whole-genome level and only a few individual linkage intervals were found to differ, all in favour of increased recombination through the male. Distorted segregations found in the three-way crosses provide evidence of post-gametic selection for particular gene(s) or chromosome regions. The significance of these results for the design of pearl millet breeding programmes and inheritance experiments, as well as for other experimental strategies, is discussed.

Resistance gene deployment strategies in cereal hybrids using marker-assisted selection: gene pyramiding, three-way hybrids, and synthetic parent populations.

Marker-assisted selection (MAS) for resistance genes (R-genes), identified using molecular markers and quantitative trait loci (QTL) analysis, is now possible in many crops. MAS can be used to pyramid several R-genes into a single host genotype. However, this may not provide durable genetic resistance because the pathogen is exposed to a full homozygous pyramid during hybrid seed production and to a full heterozygous pyramid in the resultant hybrid. Alternative gene deployment strategies that generate genetic variability were analysed, for hybrid cereal cultivars of pearl millet, maize, sorghum and rice, using maintainer lines (B-lines) with two smaller complementary pyramids. An F1 seed parent, produced on two such B-lines, can be used to produce a three-way hybrid. All target loci are heterozygous for resistance alleles in the F1 seed parent, and the pathogen is exposed in the hybrid to a host population that is heterogeneous and heterozygous for alleles at the resistance loci targeted by MAS. Alternatively, single-cross hybrids can be made on seed parents that are maintained by two B-lines that differ for the complementary resistance gene pyramids. In a cross-pollinated crop, the B-lines are allowed to intermate to produce a synthetic B-line. In an inbreeding crop, the B-lines are equivalent to a two-component multiline variety. In inbreeding crops, because there is no intermating between the B-line components, the resultant synthetic seed parents have a higher frequency of genotypes with resistance alleles (R-alleles) at several resistance loci. However, in both cross-pollinated and inbreeding crops the genotypic structure in the hybrids is almost the same. All alternatives to a single-cross hybrid having a full pyramid produce hybrid cultivars having lower frequencies of resistance alleles. The frequency of genotypes having R-alleles at several loci increases greatly in both seed parent and hybrid when the overall frequency of R-alleles in the maintainer lines increases. This is simply done by adding a maintainer line that has a full pyramid or by the component lines having overlapping pyramids.

How narrowly adapted are the products of decentralised breeding? The spread of rice varieties from a participatory plant breeding programme in Nepal

Acceptable rice varieties for high-altitude areas of Nepal were bred by participatory plant breeding (PPB). One of the most adopted varieties, Machhapuchhre-3 (M-3), performed much better in the formal trials system than the products from centralised breeding and was released in 1996. From 1996 to 1999, the spread of M-3 was monitored in high-altitude villages along with unreleased variety Machhapuchhre-9 (M-9), derived from the same cross. The study was done by interviewing individual households, groups, and field verification. Both M-3 and M-9 spread from farmer-to-farmer and through interventions by Non-Government Organisations (NGOs) and Government Organisations (GOs). Their adoption had steadily increased and their spread commenced five to six years earlier than would have been the case in a conventional system. The PPB programme was decentralised – all selection was in only two villages in the same valley – but this did not result in specific adaptation. The varieties were adopted in distant villages situated at much lower altitudes to the original PPB sites and the greatest yield advantage of the varieties over the local landraces was also at these lower altitudes.