Publications by authors named "Simon Diffey"

9 Publications

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Interplay between grain digestion and fibre in relation to gastro-small-intestinal passage rate and feed intake in pigs.

Eur J Nutr 2021 May 5. Epub 2021 May 5.

Australian Research Council, Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia.

Purpose: 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.

Method: 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.

Result: MRT was affected by grain-type/processing (P < 0.05) and fibre amount (P < 0.05). An approximate tenfold increase in ADC showed a limited decline in MRT (P = 0.18). OH at 20% increased MRT (P < 0.05) and reduced FI (P < 0.05). Ileal digestibility of starch increased and faecal SCFA concentration decreased with ADC; values for MS being lower (P < 0.001) and higher (P < 0.05), respectively, than for SFW.

Conclusions: Lower ileal digestibility of starch, higher faecal SCFA concentration and longer MRT of MS than SFW, suggest the ileal/colonic brakes may be operating. FI appeared to decrease with increasing MRT. MRT increased and intake decreased with grain-based foods/feeds that have low starch digestibility and substantial amounts of insoluble fibre.
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http://dx.doi.org/10.1007/s00394-021-02567-3DOI Listing
May 2021

Post-mortem pH decline in lamb semitendinosus muscle and its relationship to the pH decline parameters of the longissimus lumborum muscle: A pilot study.

Meat Sci 2021 Jun 20;176:108473. Epub 2021 Feb 20.

Centre for Red Meat and Sheep Development, NSW Department of Primary Industries, Cowra, New South Wales 2794, Australia.

This study compared longissimus lumborum (LL) and semitendinosus (ST) muscles, in 48 lamb carcasses, to determine their pH decline parameters and achievement of ideal pH criteria (hitting the window). These include the pH at temperature 18 °C ([email protected]) and temperature at pH 6 ([email protected]). No practical difference were found between muscles for [email protected] or the [email protected], although there were differences between the experimental carcasses evaluated. Indeed, for all but three carcasses, there were insignificant differences between the LL and ST in terms of their [email protected] This outcome suggests that the lower value and more accessible ST muscle can be measured to determine lamb carcass pH decline parameters, instead of the LL. Because of the scale of this study, additional investigation is advised prior to any adoption.
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http://dx.doi.org/10.1016/j.meatsci.2021.108473DOI Listing
June 2021

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.).

Sci Rep 2020 03 10;10(1):4416. Epub 2020 Mar 10.

NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.

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.
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http://dx.doi.org/10.1038/s41598-020-61211-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064481PMC
March 2020

Wheat bran and oat hulls have dose-dependent effects on ad-libitum feed intake in pigs related to digesta hydration and colonic fermentation.

Food Funct 2019 Dec;10(12):8298-8308

Australian Research Council, Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, 4072, Australia.

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.
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http://dx.doi.org/10.1039/c8fo02496kDOI Listing
December 2019

Stable Quantitative Resistance Loci to Blackleg Disease in Canola ( L.) Over Continents.

Front Plant Sci 2018 23;9:1622. Epub 2018 Nov 23.

IGEPP, INRA, Agrocampus Ouest, Université Rennes, Le Rheu, France.

The hemibiotrophic fungus, is the most devastating pathogen, causing blackleg disease in canola ( L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-/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-' 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 which is present in 'Darmor-' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several 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-' 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.
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http://dx.doi.org/10.3389/fpls.2018.01622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265502PMC
November 2018

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

Front Plant Sci 2016 24;7:1513. Epub 2016 Oct 24.

Marcroft Grains Pathology, Horsham VIC, Australia.

Key message "We identified both quantitative and quantitative resistance loci to , 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 One of the novel loci identified for the first time, , conveys adult plant resistance in canola." Blackleg, caused by , is a significant disease which affects the sustainable production of canola (). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to . 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 / 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 . One of the novel loci identified for the first time, , conveys adult plant resistance and mapped within 13.2 kb from gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of genes of and on the sequenced genome of cv. Darmor-. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to in canola.
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http://dx.doi.org/10.3389/fpls.2016.01513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075532PMC
October 2016

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

PLoS One 2014 9;9(7):e101673. Epub 2014 Jul 9.

Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101673PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090071PMC
March 2015

SNP markers-based map construction and genome-wide linkage analysis in Brassica napus.

Plant Biotechnol J 2014 Sep 3;12(7):851-60. Epub 2014 Apr 3.

Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia.

An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.
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http://dx.doi.org/10.1111/pbi.12186DOI Listing
September 2014

Genetic control of wheat quality: interactions between chromosomal regions determining protein content and composition, dough rheology, and sponge and dough baking properties.

Theor Appl Genet 2009 May 13;118(8):1519-37. Epub 2009 Mar 13.

CSIRO Plant Industry and the Food Futures Flagship, GPO BOX 1600, Canberra, ACT, 2601, Australia.

While the genetic control of wheat processing characteristics such as dough rheology is well understood, limited information is available concerning the genetic control of baking parameters, particularly sponge and dough (S&D) baking. In this study, a quantitative trait loci (QTL) analysis was performed using a population of doubled haploid lines derived from a cross between Australian cultivars Kukri x Janz grown at sites across different Australian wheat production zones (Queensland in 2001 and 2002 and Southern and Northern New South Wales in 2003) in order to examine the genetic control of protein content, protein expression, dough rheology and sponge and dough baking performance. The study highlighted the inconsistent genetic control of protein content across the test sites, with only two loci (3A and 7A) showing QTL at three of the five sites. Dough rheology QTL were highly consistent across the 5 sites, with major effects associated with the Glu-B1 and Glu-D1 loci. The Glu-D1 5 + 10 allele had consistent effects on S&D properties across sites; however, there was no evidence for a positive effect of the high dough strength Glu-B1-al allele at Glu-B1. A second locus on 5D had positive effects on S&D baking at three of five sites. This study demonstrated that dough rheology measurements were poor predictors of S&D quality. In the absence of robust predictive tests, high heritability values for S&D demonstrate that direct selection is the current best option for achieving genetic gain in this product category.
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http://dx.doi.org/10.1007/s00122-009-1000-yDOI Listing
May 2009