Katherine A. Steele

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.

A combined RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs for root-penetration ability.

Abstract Acombined RFLP and AFLP linkage map of an F6 recombinant inbred population, which was derived from a previously mapped F2 of a cross between the two drought resistant upland rice varieties Bala and Azucena, is presented. The map contains 101 RFLP and 34 AFLP markers on 17 linkage groups covering 1680 cM. Also presented is the approximate mapping position of a further four RFLP and 75 AFLP markers, which either could not be given a unique place on the map or for which the available data is not sufficient to allow confident positioning, and the result of quantitative trait locus (QTL) mapping of traits related to root-penetration ability. Root penetration was assessed by counting the number of root axes that penetrated a 3 mm-thick layer consisting of 80% wax and 20% white soft paraffin. Good root penetration would be expected to increase drought resistance where soil strength is high. Single-marker analysis revealed seven QTLs for the number of roots which penetrate the wax layer. In identical locations were seven QTLs for the ratio of penetrated to the total number of roots. Transgressive inheritance of positive alleles from Bala explained four of these QTLs. Comparison of the QTLs identified here with previous reports of QTLs for root morphology suggest that alleles which improve root penetration ability may also either make the roots longer or thicker.

Dynamic quantitative trait loci for salt stress components on chromosome 1 of rice

Rice varieties Co39 and Moroberekan differ for leaf Na+ concentrations when grown at moderate salinity (100–150 mol m–3 NaCl; 10 : 1 or 20 : 1 Na+ to Ca2+ ratio). Recombinant inbred lines (RILs) from a cross between them were used to map quantitative trait loci (QTL) under salt stress over several weeks. Two experiments (conducted with 170 and 96 RILs, and a linkage map of 126 RFLP markers) identified a major effect on QTL for leaf Na+ concentration and K+ : Na+ ratio on chromosome 1 in a region corresponding to 11.07–14.6 Mbp. No leaf Cl– QTL were detected. In a third experiment, leaves and sheaths were harvested after 7 and 21 days at 100 mol m–3 NaCl. The linkage map of chromosome 1 was improved by the addition of 28 microsatellite markers, which resolved distinct QTL for Na+ and K+ concentrations, and K+ : Na+ ratio. After 7 days’ stress, the most significant QTL were in the region of 11.56–12.66 Mbp. The highest Na+ concentrations were recorded in the sheaths. Na+ concentration QTL were detected for leaves, but not for sheaths. After 21 days’ stress, the region containing the most significant QTL extended to 11.07 Mbp in leaves and in sheaths. A QTL for the ratio of leaf Na+ to sheath Na+ concentrations was found at 11.39–12.39 Mbp. These findings suggest that multiple genes in this region are involved in the response to salinity, and their impact is dynamic according to stress duration, and leaf age and type.

Participatory Breeding For Drought and Salt Tolerant Crops

Although enormous effort has been put into conventional breeding programmes for both drought and salt tolerance, there has been little progress in producing varieties that are adopted by farmers in their fields. This is largely due to the lack of consideration given to the specific needs of farmers in droughted and salt-affected environments, in particular in terms of non-yield post-harvest traits. We discuss with examples the advantages and disadvantages of participatory variety selection (PVS) and participatory plant breeding (PPB) in their various forms, as well as the use of the term client-oriented breeding to describe the process of involving the end-users of the breeding programme. Methods for the analysis of participatory trials, and practical considerations for their management, are presented. We also show how both participatory and molecular approaches can be combined into an integrated, client-oriented breeding programme

Morphological and AFLP diversity in Thaumatococcus daniellii , the source of the protein sweetener thaumatin

Thaumatococcus daniellii is a perennial African wild edible plant. Fruit arils from natural populations are the source of the protein sweetener, thaumatin. There are relatively few documented examples of its cultivation, however it has great potential as an intercrop for cultivation under rubber or cocoa. Across the species range there is notable diversity in leaf and fruit morphology. In this study, T. daniellii populations from four provenances in Ghana and Cameroon (separated by the Dahomey Gap) were compared for leaf and fruit morphology in situ and in an experiment using plants grown from sampled rhizomes planted under rubber in a single location in Cameroon. When collected rhizomes from four provenances were planted at one location, the samples from the local provenance produced the largest plants and fruits, and there was less morphological variation between samples from different provenances than was recorded in situ. In situ morphological differences were notable between north–south separated provenances in each country. Fruit collected in situ was analysed for aril thaumatin content and significant variation was found between provenances (1.08–2.00%). Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among the four provenances and 54% of loci were polymorphic. Cluster analysis of AFLP data separated samples of T. daniellii according to geographical origin. Maximum genetic diversity was found between provenances separated across the Dahomey Gap.

Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice

Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci. KASP is a cost-effective single-step genotyping technology, cheaper than SSRs and more flexible than genotyping by sequencing (GBS) or array-based genotyping when used in selection programmes. Before this study, there were 2015 rice KASP marker loci in the public domain, mainly identified by array-based screening, leaving large proportions of the rice genome with no KASP coverage. Here we have addressed the urgent need for a wide choice of appropriate rice KASP assays and demonstrated that NGS can detect many more KASP to give full genome coverage. Through re-sequencing of nine indica rice breeding lines or released varieties, this study has identified 2.5 million variant sites. Stringent filtering of variants generated 1.3 million potential KASP assay designs, including 92,500 potential functional markers. This strategy delivers a 650-fold increase in potential selectable KASP markers at a density of 3.1 per 1 kb in the indica crosses analysed and 377,178 polymorphic KASP design sites on average per cross. This knowledge is available to breeders and has been utilised to improve the efficiency of public sector breeding in Nepal, enabling identification of polymorphic KASP at any region or quantitative trait loci in relevant crosses. Validation of 39 new KASP was carried out by genotyping progeny from a range of crosses to show that they detected segregating alleles. The new KASP have replaced SSRs to aid trait selection during marker-assisted backcrossing in these crosses, where target traits include rice blast and BLB resistance loci. Furthermore, we provide the software for plant breeders to generate KASP designs from their own datasets.

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait.