Catherine J. Howarth

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.

Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions

Abstract  Drought stress during the reproductive stage is one of the most important environmental factors reducing the grain yield and yield stability of pearl millet. A QTL mapping approach has been used in this study to understand the genetic and physiological basis of drought tolerance in pearl millet and to provide a more-targeted approach to improving the drought tolerance and yield of this crop in water-limited environments. The aim was to identify specific genomic regions associated with the enhanced tolerance of pearl millet to drought stress during the flowering and grain-filling stages. Testcrosses of a set of mapping-population progenies, derived from a cross of two inbred pollinators that differed in their response to drought, were evaluated in a range of managed terminal drought-stress environments. A number of genomic regions were associated with drought tolerance in terms of both grain yield and its components. For example, a QTL associated with grain yield per se and for the drought tolerance of grain yield mapped on linkage group 2 and explained up to 23% of the phenotypic variation. Some of these QTLs were common across stress environments whereas others were specific to only a particular stress environment. All the QTLs that contributed to increased drought tolerance did so either through better than average maintenance (compared to non-stress environments) of harvest index, or harvest index and biomass productivity. It is concluded that there is considerable potential for marker-assisted backcross transfer of selected QTLs to the elite parent of the mapping population and for their general use in the improvement of pearl millet productivity in water-limited environments.

Genomic regions associated with grain yield and aspects of post-flowering drought tolerance in pearl millet across stress environments and tester background

A pearl millet mapping population from a cross between ICMB841 and 863B was studied for DNA polymorphism to construct a genetic linkage map, and to map genomic regions associated with grain and stover yield, and aspects of drought tolerance. To identify genomic regions associated with these traits, mapping population testcrosses of 79 F3 progenies were evaluated under post-flowering drought stress conditions over 2 years and in the background of two elite testers. A significant genotype × drought stress treatment interaction was evident in the expression of grain and stover yield in drought environments and in the background of testers over the 2 years. As a result of this, genomic regions associated with grain and stover yield and the aspects of drought tolerance were also affected: some regions were more affected by the changes in the environments (i.e. severity and duration of drought stress) while others were commonly identified across the drought stress environments and tester background used. In most instances, both harvest index and panicle harvest index co-mapped with grain yield suggesting that increased drought tolerance and yield of pearl millet that mapped to these regions was achieved by increased partitioning of dry matter from stover to the grains. Drought stress treatments, years and testers interactions on genomic regions associated with grain and stover yield of pearl millet are discussed, particularly, in reference to genetic improvement of drought tolerance of this crop using marker-assisted selection.

Mapping and characterisation of QTL × E interactions for traits determining grain and stover yield in pearl millet

Abstract.A mapping population of 104 F3 lines of pearl millet, derived from a cross between two inbred lines H 77/833-2 × PRLT 2/89-33, was evaluated, as testcrosses on a common tester, for traits determining grain and stover yield in seven different field trials, distributed over 3 years and two seasons. The total genetic variation was partitioned into effects due to season (S), genotype (G), genotype × season interaction (G × S), and genotype × environment-within-season interaction [G × E(S)]. QTLs were determined for traits for their G, G × S, and G × E(S) effects, to assess the magnitude and the nature (cross over/non-crossover) of environmental interaction effects on individual QTLs. QTLs for some traits were associated with G effects only, while others were associated with the effects of both G and G × S and/or G, G × S and G × E(S) effects. The major G × S QTLs detected were for flowering time (on LG 4 and LG 6), and mapped to the same intervals as G × S QTLs for several other traits (including stover yield, harvest index, biomass yield and panicle number m–2). All three QTLs detected for grain yield were unaffected by G × S interaction however. All three QTLs for stover yield (mapping on LG 2, LG 4 and LG 6) and one of the three QTLs for grain yield (mapping on LG 4) were also free of QTL × E(S) interactions. The grain yield QTLs that were affected by QTL × E(S) interactions (mapping on LG 2 and LG 6), appeared to be linked to parallel QTL × E(S) interactions of the QTLs for panicle number m–2 on (LG 2) and of QTLs for both panicle number m–2 and harvest index (LG 6). In general, QTL × E(S) interactions were more frequently observed for component traits of grain and stover yield, than for grain or stover yield per se.

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

Effects of High Soil Surface Temperature on Seedling Survival in Pearl Millet

A field technique to screen pearl millet genotypes for their emergence and survival at high soil surface temperatures is described. Genetic variation in seedling emergence and survival is shown and it is argued that this variation is largely due to tolerance of high temperatures rather than tolerance of soil moisture deficit, although some interaction occurred. An index for ‘thermotolerance’ is defined and genotypes are ranked accordingly for this trait, which is shown to be highly heritable. The technique is repeatable and allows a large number of genotypes to be screened at the same time.

Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template. For each of the sorghum QTL regions, the reported RFLP markers were compiled, used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL, on chromosome 9 for Stg3 QTL, and on chromosome 11 for Stg4 QTL. Using the Gramene genome browsing tool, 869 non-redundant sorghum expressed sequence tags (ESTs) were selected and 50 genic-microsatellites (18, 12, 15, and 5, for Stg1, Stg2, Stg3, and Stg4 QTL, respectively) could be developed. We could experimentally establish synteny of the Stg1, Stg2, Stg3, and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers (20%) to the positions of the staygreen QTL. The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family. The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach, and create an additional option for MAS of the staygreen trait in sorghum.

Genetic Diversity and Population Structure Among Oat Cultivars and Landraces

In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.

A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement

We constructed a hexaploid oat consensus map from 12 populations representing 19 parents. The map represents the most common physical chromosome arrangements in oat. Deviations from the consensus map may indicate physical rearrangements. Large chromosomal translocations vary among different varieties. There is regional synteny with rice but considerable subgenome rearrangement.

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

Key messageGenome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat.AbstractWe investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.