A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al3+ resistance in Brassica napus

Acid soils limit yields of many important crops including canola (Brassica napus ), Australia's third largest crop. Aluminium (Al3+ ) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12μM, pH 4.3) for 12days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus , 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus . The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.

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

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.

Novel Sources of Tolerance to Aluminium Toxicity in Wild Cicer (Cicer reticulatum and Cicer echinospermum) Collections

In acid soils, the toxic form of aluminium, Al³⁺, significantly inhibits root growth and elongation, leading to less water and nutrient uptake. Previous research had shown differential Al toxicity tolerance among cultivated Cicer arietinum L. (chickpea); however, the potential for developing tolerant cultivars is limited by the narrow genetic diversity of cultivated chickpeas. Recent collections from Turkey of wild Cicer species, Cicer reticulatum, and Cicer echinospermum, have increased the available gene pool significantly, but there has been no large-scale screening of wild Cicer for acid tolerance or Al³⁺ toxicity tolerance. This study evaluated 167 wild Cicer and 17 Australian chickpea cultivars in a series of screenings under controlled growth conditions. The pH of 4.2 and Al concentrations of 15 and 60 μM Al were selected for large-scale screening based on dose response experiments in a low ionic strength nutrient solution. The change in root length showed better discrimination between tolerant and sensitive lines when compared with shoot and root dry weights and was used as a selection criterion. In a large-scale screening, 13 wild Cicer reticulatum accessions had a higher root tolerance index (≥50%), and eight had higher relative change in root length (≥40%) compared with PBA Monarch, which showed greater tolerance among the Australian domestic cultivars screened. In general, C. reticulatum species were found to be more tolerant than C. echinospermum, while genetic population groups Ret_5, Ret_6, and Ret_7 from Diyarbakir and Mardin Province were more tolerant than other groups. Among C. echinospermum, Ech_6 from the Siv-Diyar collection site of the Urfa Province showed better tolerance than other groups. In this first detailed screening of aluminium toxicity tolerance in the new wild Cicer collections, we identified accessions that were more tolerant than current domestic cultivars, providing promising germplasm for breeding programs to expand chickpea adaptation to acid soils.

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

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.

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

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.

Predicting the nutritional quality of feed ingredients for pigs using near-infrared spectroscopy (NIRS) and chemical analysis

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.

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.

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.

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

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.

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.

Localisation of quantitative trait loci for quality attributes in a doubled haploid population of wheat (Triticum aestivum L.)

Selection of wheat germplasm for a range of quality traits has been a challenging exercise because of the cost of testing, the variation within testing data, and a poor understanding of the underlying genetics. The objective of this study was to identify quantitative trait loci (QTLs) underlying quality traits in wheat. A doubled haploid population comprising 190 lines from Chara/WW2449 was grown in two different environments and evaluated for various quality traits. A molecular map comprising 362 markers based upon simple sequence repeat, sequence tagged microsatellite, glutenin, and DArT loci was constructed and subsequently exploited to identify QTLs using a whole-genome approach. Fifteen QTLs that were consistent in the two different environments were identified for thousand kernel mass, grain protein content, milling yield, flour protein content, flour colour, flour water absorption, dough development time, dough strength (extensograph height and resistance at 5 cm), and dough extensibility (extensograph length) using the whole genome average interval mapping approach. The amount of genetic variation explained by individual QTLs ranged from 3% to 49%. A number of QTLs associated with dough strength, dough extensibility, dough development time, and flour water absorption were located close to the glutenin Glu-B1 locus on chromosome 1B. Identification of the chromosomal location and effect of the QTLs influencing wheat quality may hasten the development of superior wheats for target markets via marker-assisted selection.

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

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.

Influences of field pea (Pisum sativum) density on grain yield and competitiveness with annual ryegrass (Lolium rigidum) in south-eastern Australia

The variation in field pea grain yield and competitiveness with annual ryegrass due to crop density, row spacing and cultivar was determined to enable farmers to better manage weeds with cultural control tactics. Crop density varied with seeding rate, cultivar, row spacing and year. Higher seeding rates were required to reach equivalent plant densities in cv. Dinkum (short, semi-leafless) compared with cv. Dundale (tall, conventional-leaf), and at 36 cm compared with 18 cm row spacing. Field pea grain yield was reduced more at low crop densities, in Dinkum, at 36 cm row spacing, and in the presence of weeds. Percentage yield losses from weed competition were similar in both cultivars (about 70–80%) at a low density of 10 plants/m2 in 2 seasons. At higher crop densities Dinkum had a larger loss than Dundale (i.e. at 30 plants/m2 losses were 60 and 35%, respectively, compared with 50 and 5% at 60 plants/m2). Seasonal variation influenced the effect of crop density on yield loss from weeds. The percentage yield loss from weeds in 1993 ranged from about 90 to 40% at plant densities of 10 to 40 plants/m2, in contrast to 1995 when 40% yield loss occurred at all these densities. Ryegrass dry weight was reduced with increasing field pea density in both years, and in the tall more than the short cultivar in 1 year. Maintaining recommended field pea seeding rates has considerable financial benefits in both weed-free (around $100/ha) and weed-affected crops (to $400/ha). In weedy situations, integrating cultural practices such as higher seeding rates and choice of cultivar that enhance crop competitiveness will improve weed management in south-eastern Australia.