A strategy to develop molecular markers applicable to a wide range of crosses for marker assisted selection in plant breeding: a case study on anthracnose disease resistance in lupin (Lupinus angustifolius L.)

A key challenge in marker-assisted selection (MAS) for molecular plant breeding is to develop markers linked to genes of interest which are applicable to multiple breeding populations. In this study representative F₂ plants from a cross Mandalup (resistant to anthracnose disease) × Quilinock (susceptible) of Lupinus angustifolius were used in DNA fingerprinting by Microsatellite-anchored Fragment Length Polymorphism (MFLP). Nine candidate MFLP markers linked to anthracnose resistance were identified, then ‘validated’ on 17 commercial cultivars. The number of “false positives” (showing resistant-allele band but lack of the R gene) for each of the nine candidate MFLP markers on the 17 cultivars ranged from 1 to 9. The candidate marker with least number of false positive was selected, sequenced, and was converted into a co-dominant, sequence-specific, simple PCR based marker suitable for routine implementation. Testing on 180 F₂ plants confirmed that the converted marker was linked to the R gene at 5.1 centiMorgan. The banding pattern of the converted marker was consistent with the disease phenotype on 23 out of the 24 cultivars. This marker, designated “AnManM1”, is now being used for MAS in the Australian lupin breeding program. We conclude that generation of multiple candidate markers, followed by a validation step to select the best marker before conversion to an implementable form is an efficient strategy to ensure wide applicability for MAS.     

Rapid thermal adaptation in photosymbionts of reef‐building corals

Climate warming is occurring at a rate not experienced by life on Earth for 10 s of millions of years, and it is unknown whether the coral‐dinoflagellate (Symbiodinium spp.) symbiosis can evolve fast enough to ensure coral reef persistence. Coral thermal tolerance is partly dependent on the Symbiodinium hosted. Therefore, directed laboratory evolution in Symbiodinium has been proposed as a strategy to enhance coral holobiont thermal tolerance. Using a reciprocal transplant design, we show that the upper temperature tolerance and temperature tolerance range of Symbiodinium C1 increased after ~80 asexual generations (2.5 years) of laboratory thermal selection. Relative to wild‐type cells, selected cells showed superior photophysiological performance and growth rate at 31°C in vitro, and performed no worse at 27°C; they also had lower levels of extracellular reactive oxygen species (exROS). In contrast, wild‐type cells were unable to photosynthesise or grow at 31°C and produced up to 17 times more exROS. In symbiosis, the increased thermal tolerance acquired ex hospite was less apparent. In recruits of two of three species tested, those harbouring selected cells showed no difference in growth between the 27 and 31°C treatments, and a trend of positive growth at both temperatures. Recruits that were inoculated with wild‐type cells, however, showed a significant difference in growth rates between the 27 and 31°C treatments, with a negative growth trend at 31°C. There were no significant differences in the rate and severity of bleaching in coral recruits harbouring wild‐type or selected cells. Our findings highlight the need for additional Symbiodinium genotypes to be tested with this assisted evolution approach. Deciphering the genetic basis of enhanced thermal tolerance in Symbiodinium and the cause behind its limited transference to the coral holobiont in this genotype of Symbiodinium C1 are important next steps for developing methods that aim to increase coral bleaching tolerance.     

Potential biases in screening for plant resistance to insect pests: an illustration with oilseed rape

Breeding to increase crop resistance is a common strategy to decrease damage caused by insect pests, especially in the current context where insecticides are becoming at the same time less accepted by society and less efficient because of widespread pest resistance. The main bottleneck of this strategy is phenotyping. Although simple, high‐throughput methods have been proposed which could be highly useful, they may raise conceptual issues. Using field and laboratory experiments on oilseed rape (Brassica napus) and the pollen beetle (Brassicogethes aeneus syn. Meligethes aeneus), we illustrated possible difficulties with this approach: (i) field screenings might not represent the real attractiveness of the tested genotypes; (ii) plant phenology or spatial organization of the genotypes might bias field screening results; (iii) experiments based on detached plant parts (here, single flower buds or anthers) might not allow to infer the plant–insect relationship of the whole plant. We propose ways to better take these risks into account.     

Smallholder experiences with dairy cattle crossbreeding in the tropics: from introduction to impact

Crossbreeding of indigenous tropical and improved western dairy cattle breeds as tool to improve dairy cattle performance on smallholder farms has been widely advocated, criticised and yet applied. The government of Ethiopia supported this technology for decades but adoption rate is low. Constraints are documented but there is little information about farm level introduction and development of crossbreeding. A total 122 smallholders with mixed crop livestock farms and at least 8 years of successful crossbreeding were interviewed using a pre-tested questionnaire in two contexts in Amhara Regional state in north-western Ethiopia. Crossbreeding initiator was either uncoordinated government extension or a coordinated development project, also implemented with governmental support. Qualitative and quantitative data on farmers’ motivations, crossbreeding introduction, initiator support, breeding adaptation and impacts at farm level were analysed. Results show that even though motives vary between contexts the underlying reason to introduce crossbreeding was economic profit. To be able to introduce crossbreeding support of initiators (e.g. extension) and other farmers was essential. The crossbreeding introduction context had some influence. Governmental actors were the main source of support and supplier of exotic genetics but the farmer network acted as safety net filling gaps of government support. Breeding strategies focused on performance increase. A lack of basic understanding of crossbreeding has been identified. A surprising, probably biased, result was general satisfaction with initiator support and with breeding services. It was challenged by the high proportion of farmers unable to follow a breeding strategy due to insufficient bull and/or semen supply. Crossbreeding changed the smallholder production system to a high input – high output system. Except for crossbred adaptation problems, challenges were ranked context specific and influenced by the initiator. Farmers perceived crossbreeding as success and recommended it. We conclude that farmers can realize income increase with crossbreeding. The complexity of this technology, high initial investment and the need for support services and external production inputs are probable reasons why crossbreeding uptake is low. Improving the availability of semen and/or bulls must be the top priority for breeding service providers to enable farmers to follow a breeding strategy and reach a suitable and sustainable herd performance. Access to investment capital, input supply, strong technical support and market linkages are crucial for successful crossbreeding.     

Enhancing crop legume N2 fixation through selection and breeding

Legume N₂ fixation is variable, but nonetheless is a valuable process in world agriculture. There is great potential to increase the contribution by the crop legumes to the world's supply of soil.N. This will be achieved by (i) increasing the area of legumes sown by farmers; (ii) improved management of the crops in order that the major determinants of productivity, e.g. land area, water availability, are converted to harvested product with maximum efficiency; and (iii) genetic modification of the commonly-grown species to ensure high dependence of the legume crop on N₂ fixation at all levels of productivity. Currently-used methods for measuring N₂ fixation and for assessing heritability and repeatability of N₂ fixation in breeding and selection programs are reviewed. Results from research programs to define genetic variation in N₂ fixation and to enhance N₂ fixation through selection and breeding are presented with particular emphasis on common bean (Phaseolus vulgaris) and soybean (Glycine max).     

Integrating climate change and habitat fragmentation to identify candidate seed sources for ecological restoration

Anthropogenic change (climate change and habitat fragmentation) is driving a growing view that local seed collections may need to be supplemented with nonlocal seed as a strategy to bolster genetic diversity and thus increase evolutionary potential of plantings. While this strategy is becoming widely promoted, empirical support is limited, and there is a lack of accessible research tools to assist in its experimental testing. We therefore provide the Provenancing Using Climate Analogues (PUCA) framework that integrates the principles of the climate‐adjusted provenancing strategy with concepts from population genetics (i.e. potential inbreeding in small fragmented populations) as both a research and operational‐ready tool to guide the collection of nonlocal seed. We demonstrate the application of PUCA using the Midlands of Tasmania, Australia, a region that is currently undergoing large‐scale ecological restoration. We highlight multiple nonlocal seed sources for testing by identifying actual species distribution records that currently occupy environments similar to that projected to occur at the restoration site in the future. We discuss the assumptions of PUCA and the ecological considerations that need to be tested when moving nonlocal genotypes across the landscape.