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The combined effects of grain digestibility and dietary fibre on digesta passage rate and satiety in humans are poorly understood. Satiety can be increased through gastric distention, reduced gastric emptying rate and when partially digested nutrients reach the terminal ileum to stimulate peptide release through the ileal/colonic brakes to slow the rate of digesta passage. This study determined the effects of grain digestibility and insoluble fibre on mean retention time (MRT) of digesta from mouth-to-ileum, feed intake (FI), starch digestion to the terminal ileum and faecal short chain fatty acids (SCFA) in a pig model. Twelve grain-based [milled sorghum (MS), steam-flaked-sorghum, milled wheat, and steam-flaked-wheat (SFW)] diets with different intrinsic rates of starch digestion, assessed by apparent amylase diffusion coefficient (ADC), and fibre from oat hulls (OH) at 0, 5 and 20% of the diet were fed to ileal-cannulated pigs. MRT was affected by grain-type/processing (P

Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the ‘ascospore shower’ test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.

Undigested nutrients and fermentable fibre in the distal ileum and colon stimulate intestinal brakes, which reduce gastric-emptying and digesta-passage-rate, and subsequently limit feed/food-intake. Fibre can also stimulate passage rate potentially increasing feed intake (FI). In order to experimentally determine the relationships between these two hypothesised actions of fibre, five levels of wheat-bran (WB) or oat-hulls (OH) were added to a highly digestible starch-based diet fed to pigs ad-libitum for three weeks. Average-daily-feed-intake (ADFI), faecal short-chain-fatty-acids (SCFA) and related parameters were determined at 7, 14 and 21d. A linear mixed model was fitted to FI and fermentation parameters. Overall, WB diets showed 8-11% lower ADFI (7-14d: p < 0.05; 7-21 & 0-21d: p = 0.053) than OH diets. WB diets produced over 20% more (21d: p < 0.01) SCFA than OH or Control diets. WB at 25% produced 22% more (7d: p < 0.05) SCFA than any other diet. Diets with WB at 25 and 35%, showed higher hydration capacity than any other diet (p < 0.001). OH at 10% had an unusually low FI and a markedly higher hydration capacity. With increasing levels of OH, intake of base diet was 7% more than control at 5% OH, but 8% less than control at 20% OH. With increasing WB content, intake of base diet decreased. From these results, we propose that three mechanisms control the effects of fibre on FI: initial increase in passage rate and feed intake at low concentrations of non-swelling fibres; a depression in FI from high fibre bulk; and reduced feed intake from stimulation of ileal and colonic brakes.

Multi-environment wheat trials provide valuable information on the extent of genotype x environment interaction, the stability of genotypes and define and confirm agro-ecological regions through associations among sites. The All India Coordinated Crop Improvement Project on wheat evaluates candidates for release across the wheat growing regions of India. To facilitate this process the wheat area is divided into six agro-ecological zones; the northwestern plains zone (NWPZ), the northeastern plains zone (NEPZ), the central zone (CZ), the peninsular zone (PZ), the northern hills zone (NHZ) and the southern hills zone (SHZ). Factor analytic (FA) models were used to analyze the genotype x environment interaction for yield of 813 wheat genotypes evaluated at 136 locations across the six agro-ecological zones in 1307 individual advanced variety trials between 2008/09 and 2012/13. Genotype x environment interaction was firstly assessed separately within each of the six established agro-ecological zones. Key locations with a high genetic correlation with all other locations within each zone were identified. Predicted genetic values of important cultivars that were represented in a wider range of environments within each zone were estimated and highly stable genotypes were found. Genotype x environment interaction was subsequently assessed across agro-ecological zones. Only those environments where the models accounted for > 99% of the genetic variance were retained for further analysis and two smaller zones (NHZ and SHZ) with little or no genotype congruence with other agro-ecological zones were removed. Thus 476 genotypes from 488 environments were included in the analysis. Fifteen clusters of environments with similar patterns of adaptation were found. These clusters were then characterized based on zonal classification, sowing time, irrigation regime, latitude and year and three regions broadly representing the main wheat growing areas of India were identified. These regions represent a combination of the NWPZ and NEPZ defined by latitude, a central region that combines CZ locations with northern PZ locations and a southern region comprised of southern PZ sites. Further stratification of these zones was then possible based on sowing time and irrigation practice. One cluster of 29 environments had a high average genetic correlation (r = 0.75) with most other environments and production zones. These represent key locations where larger numbers of entries might be grown in future seasons as they are the best predictors of yield across cropping zones.

The hemibiotrophic fungus, Leptosphaeria maculans is the most devastating pathogen, causing blackleg disease in canola (Brassica napus L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-bzh/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by 'Darmor-bzh' but 'Yudal' also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that Rlm9 which is present in 'Darmor-bzh' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several R genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference 'Darmor-bzh' genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies.

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.

Capacity to routinely, accurately and cost-effectively measure variation in the nutritional quality of feed ingredients before diet formulation represents a fundamental pillar of sustainable pork production worldwide. Factors driving sustainable pork production include pork price, feed cost, utilisation of co-products and downgraded raw materials and variation in pork production, with all being related to the definition and ultimate nutritional quality of feed ingredients. The present paper defines rapid measures of nutritional quality in feed ingredients for pigs and demonstrates the range that can exist in these parameters, specifically digestible energy of cereal grains and the reactive-lysine concentration of oilseed meals. It provides an overview of the development of near-infrared spectroscopy (NIRS) calibrations for key nutritional-quality parameters and how they are being applied by the pork industry. Adjunct ways to measure nutritional quality of feed ingredients for pigs such as the glucose-release index and how these can be used in conjunction with NIRS are reviewed. The paper reports advanced correlation analysis between chemical components and digestible-energy concentration of cereals, and how these could be used for screening of NIRS outliers, and discusses future opportunities for application of nutritional-quality analysis using NIRS calibrations, including feed intake and portable solutions. Using advanced NIRS calibrations for digestible energy in cereals and reactive lysine in oilseed meals, pork producers will ensure that they make best use of limited resources and, as a consequence, pork will remain a nutritionally accretive food source for increasingly discerning consumers worldwide.

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.