Simon Diffey

Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.

Quantitative genetic analysis of grain yield in an Australian Brassica napus doubled-haploid population

Abstract. High yield is a major objective in canola-breeding programs. We analysed the genetic determinants controlling variation in grain yield in a doubled-haploid (DH) breeding population derived from a single BC1F1 plant from the cross Skipton/Ag-Spectrum//Skipton (designated as the SAgS population). DH lines were evaluated for flowering time and yield in two replicated trials and exhibited significant genetic variation for both traits. Yield showed negative correlation with flowering time; lines that flowered earlier had higher yield than late-flowering lines. A genetic linkage map comprising 7716 DArTseq markers was constructed for the SAgS population, and a ‘bin’ map based on 508 discrete single-position (non-co-segregating) marker loci was used for quantitative trait locus (QTL) analysis. We identified 20 QTLs (LOD ≥2) associated with variation in flowering time and grain yield. Two QTLs (Qy.wwai-A7/Qdtf.wwai-A7/Qfs.wwai-A7 and Qy.wwai-C3a/Qfs.wwai-C3a) appeared repeatedly across experiments, accounting for 4.9–19% of the genotypic variation in flowering time and yield and were located on chromosomes A07 and C03. We identified 22 putative candidate genes for flowering time as well as grain yield, and all were located in a range of 935 bp to 2.97 Mb from markers underlying QTLs. This research provides useful information to be used for breeding high-yielding canola varieties by combining favourable alleles for early flowering and higher grain yield at loci on chromosomes A07, C03 and possibly on A06.

Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola

Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.

Herbicide efficacy for control of annual ryegrass (Lolium rigidum Gaud.) is influenced more by wheat seeding rate than row spacing

Abstract. Conservation cropping systems with no-till and stubble retention improve soil condition and water conservation. However, tillage is replaced by herbicides for weed control in these systems, increasing the threat of herbicide resistance. In the medium to high rainfall zones of the southern wheatbelt of Australia and under irrigation, wider row spacing is used to enable seeding into heavy stubble loads and to avoid stubble burning. Some evidence suggests that wider rows lead to reduced crop competitive ability and crop yields, greater herbicide dependence, and increased spread of resistance. Our aim was to test the hypothesis that increasing seeding rate compensated for reduced competitive ability at wider row spacings, especially when herbicide performance was suboptimal. We examined the impact of two wheat row spacings (18 and 36 cm) and five seeding rates (resulting in a range of densities of ∼80–700 plants/m2) on control of Lolium rigidum with five rates of post-emergence application of diclofop-methyl (Hoegrass®), ranging from label rate to lower rates, over two growing seasons. In the presence of L. rigidum, wheat grain yield was unaffected by row spacing but was significantly reduced at low seeding rates, especially at lower herbicide rates. Lolium rigidum was suppressed at higher crop densities but was also unaffected by row spacing. Grain yield was maximised when post-emergence herbicide was applied at 60–100% of the recommended dose at wheat densities >∼300 plants/m2. Significant levels of the weed remained in the crop at anthesis in all treatments. Weed dry matter ranged from 525 g/m2 at low crop densities and with no herbicide to 150 g/m2 with the recommended rate of herbicide and high wheat densities. The implications of manipulating crop competitive ability to improve weed control are discussed, especially in conditions where herbicide performance is unreliable due to weeds developing herbicide resistance or adverse environmental conditions.

Use of remote sensing to determine the relationship of early vigour to grain yield in canola (Brassica napus L.) germplasm

Abstract. Early crop vigour in canola, as in other crops, is likely to result in greater competition with weeds, more rapid canopy closure, improved nutrient acquisition, improved water-use efficiency, and, potentially, greater final grain yield. Laborious measurements of crop biomass over time can be replaced with newer remote-sensing technology to aid data acquisition. Normalised difference vegetation index (NDVI) is a surrogate for biomass accumulation that can be recorded rapidly and repeatedly with inexpensive equipment. In seven small-plot field experiments conducted over a 4-year period with diverse canola germplasm (n = 105), we have shown that NDVI measures are well correlated with final grain yield. We found NDVI values were most correlated with yield (r >0.7) if readings were taken when the crop had received 210–320 growing degree-days (usually the mid-vegetative phase of growth). It is suggested that canola breeders may use NDVI to objectively select for vigorous genotypes that are more likely to have higher grain yields.

Perspective: are animal scientists forgetting the scientific method and the essential role of statistics?

Animal scientists and their funding organisations need to ensure investment in research is maximised by strict adherence to the scientific method and the rigorous design and analysis of experiments. Statisticians should be considered as equals in the research process, engaged from the beginning of research projects and appropriately funded. The importance of experimental design that accounts for factors affecting the primary experiment measurement is illustrated in two examples. One shows how failure to involve a statistician at the beginning of a project resulted in considerable waste of resources. Subsequent engagement of professional statisticians with rigorous experimental design and analysis led to greatly increased precision in the standard error of an estimate for the digestible energy content of cereal grains for pigs from ± 0.35 MJ/kg to ± 0.16 MJ/kg. The other example shows the effect of the percentage of diets replicated during pelleting and of the total number of pigs required in the experiment on the P-values associated with detecting a pairwise difference between two grains differing in digestible energy content by 0.33 MJ/kg. Decisions based on these relationships have animal welfare and resource allocation implications.

Bubbles in Bread: Is the Answer in the Genes?

Abstract Composition, dough mixing, extensional rheological properties and baking properties of a set of 160 double haploid lines grown in two different environments were assessed in order to establish linkages between regions of the wheat genome and wheat quality traits. Further studies are required to rigorously test the impact of loci associated with rheological parameters on baking properties, as there are clear differences between the genetic control of rheological and baking parameters.