Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.).

Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits-in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson's correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.

Influence of diet on growth yields of rumen micro-organisms in vitro and in vivo: influence on growth yield of variable carbon fluxes to fermentation products.

The efficiency of rumen microbial production (EMP) in vitro and in vivo was examined for three roughages (lucerne (Medicago sativa L.) hay, oat (Avenia sativa L.)-berseem clover (Trifolium alexandrinum cultivar BigBee) hay and maize (Zea mays L.) crop residue (MCR)) and for five isonitrogenous (106 g crude protein (Nx6.25)/kg) diets formulated from lucerne hay, oat-berseem clover hay, MCR, soybean meal and maize grain to provide degradable intake protein for the production of 130 g microbial protein/kg total digestible nutrients. EMP in vivo was determined by intestinal purine recovery in sheep and ranged from 240 to 360 g microbial biomass/kg organic matter truly degraded in MCR and in one of the diets respectively (P<0.05). EMP in vitro was estimated by the substrate degraded : gas volume produced thereby (termed partitioning factor, PF (mg/ml)) at times of estimated peak microbial production and after 16.0 and 24.0 h of incubation. For the diets, PF values were significantly related to EMP in vivo at peak microbial production (P=0.04), but not after 16.0 (P=0.08) and 24.0 h (P=0.66). For roughages, PF values were significantly related to EMP in vivo only when measured after 16.0 h (P=0.04). For MCR and diets, a close non-linear relationship was found between PF values at peak microbial production and EMP in vivo (R(2) 0.99, P<0.0001) suggesting a maximum EMP in vivo of 0.39. Low gas production per unit substrate degraded (high PF) was associated with high EMP in vivo. The in vitro study of the products of fermentation, short-chain fatty acids, gases and microbial biomass (by purine analysis) after 16.0 h of incubation showed very strong relationships (R(2)> or =0.89, P<0.0001) between short-chain fatty acids, gases and gravimetrically measured apparent degradability. Except for maize grain, the true degradability of organic matter estimated by neutral-detergent solution treatment agreed with the sum of the products of fermentation (R(2) 0.81, P=0.0004). After 16.0 h of incubation, the synergistic effects of diet ingredient on diets were greater for microbial biomass (18 %) than for short-chain fatty acids and gas production (7 %). It is concluded that measurement of gas production only gives incomplete information about fodder quality; complementation of gas measurements by true degradability measurements is recommended.

The relationship between in vitro gas production, in vitro microbial biomass yield and 15N incorporation and its implications for the prediction of voluntary feed intake of roughages.

The relationship between in vitro gas production, concomitant in vitro apparent and true DM degradability has been examined in forty-two roughages. The partitioning of truly-degraded substrate between gas volume and microbial biomass yield and 15N incorporation into cells was also investigated. The relevance of this partitioning for the regulation of DM intake (DMI) was examined for fifty-four roughages. The results can be summarized as follows. In vitro gas production and in vitro apparent and true degradability are highly correlated (P < 0.0001), r being 0.96 and 0.95 respectively. There is an inverse relationship between in vitro gas production and microbial biomass yield (r--0.67, (P < 0.0001) and also 15N enrichment (P < 0.001) when the variables were related to a given unit of substrate truly degraded. Selecting roughages by in vitro gas production may well be a selection against maximum microbial yield and a combination of in vitro gas volume measurements with a complementary determination of the substrate truly degraded is proposed, to calculate a partitioning factor (PF) reflecting the variation of short-chain fatty acid production per unit substrate degraded. PF is calculated as the ratio, substrate truly degraded: gas produced by it. PF was highly significant (P < 0.0001) in DMI prediction when included in stepwise multiple correlations together with in vitro gas volume variables reflecting the extent and rate of gas production; 11% of the variation in DMI was accounted for by the PF. The total model, including extent and rate of gas production and the PF, accounted for 84% of the variation in DMI. Roughages producing proportionally less gas per unit substrate truly degraded had higher feed intakes.

The degradability characteristics of fifty-four roughages and roughage neutral-detergent fibres as described by in vitro gas production and their relationship to voluntary feed intake.

Fifty-four roughages of known voluntary dry-matter intakes (DMI; range 7.8-35.2 g/kg live weight per d) were examined in vitro in a gas production test. Samples (200 mg) of roughage and roughage neutral-detergent fibre (NDF) respectively were incubated in a mixed suspension of rumen contents for 96 h and the gas volumes recorded after 4, 6, 8, 12, 24, 30, 36, 48, 54, 60 and 96 h. The kinetics of gas production were derived from the volume recordings described by the exponential equation Y = A + B(l-e-ct) where A is the intercept and ideally reflects the fermentation of the soluble and readily available fraction of the feed, B describes the fermentation of the insoluble (but with time fermentable) fraction and c the fractional rate at which B is fermented per h; A + B describes total fermentation. In vitro true dry matter (TD) and NDF degradabilities (NDF-D) after 24 h incubation were also determined. Of the variation in DMI, 75% was accounted for by the in vitro gas production parameters A, B and c in stepwise multiple regressions; 82% of the variation in DMI was explained by the parameters (ANDF + BNDF) and cNDF as obtained from the incubation of roughage NDF. The rate constants (c) were less important than parameters related to the extent of gas production, accounting for only 6.5 (whole roughage) and 4.1% (NDF) of the variation in DMI. There was no statistical advantage in the use of the exponential model describing extent and rate of fermentation over some of the simple gas volume measurements: 75% of the variation in DMI was accounted for by in vitro gas production of whole roughage after 8 h of incubation. On average gas production from NDF measured from 24-96 h accounted for 81% of the variation in DMI. A combination of gas volume measurements after a short period of incubation (4-8 h) with a concomitant determination of NDF-D after many hours (> or = 24 h) can render NDF preparations and long incubation times redundant. A method is suggested to obtain two results for DMI prediction in one single incubation. Of the variation in DMI 80% was accounted for by the incubation of 500 mg whole roughage when incubation was terminated after 24 h and the residual undegraded substrate quantified.

Formation of complexes between polyvinyl pyrrolidones or polyethylene glycols and tannins, and their implication in gas production and true digestibility in in vitro techniques.

Various tannin-complexing agents have been used to study the potential adverse effects of tannins on rumen metabolism. Using a method based on turbidity formation, the binding of various tannin-complexing agents (polyvinyl polypyrrolidone (PVPP), polyethylene glycol (PEG) of molecular weights 2000 to 35,000, and polyvinyl pyrrolidone (PVP) of molecular weight 10,000, 40,000 and 360,000) to tannins (tannic acid, purified tannins from quebracho (Aspidosperma quebracho) and leaves of trees and shrubs (Acioa barteri, Dichostachys cinerea, Guiera senegalensis, Piliostigma reticulatum)) was investigated at different pH values. The binding of all the tannins with PVPP was highest at pH 3-4 and lowest at pH 7. For all the pH range (3-7) studied, the binding of PEG was higher than that of PVP. For all the tannins except tannic acid, the binding to PVP was the same from pH 4.7 to 7. Similar results were observed for the PEG of molecular weight 6000 or higher for all the tannins except quebracho tannins for which the binding increased as the pH increased from 3 to 7. The binding with PEG 2000 decreased to a greater extent as the pH reached near neutral and for PEG 4000 this decrease was slightly lower. Addition of these tannin-complexing agents to the in vitro gas system resulted in higher gas production from tannin-rich feeds (increase varied from 0 to 135%). The PEG were the most effective followed by PVP and PVPP. The PEG 35,000 was least effective. The efficiency of other PEG was similar. The PEG 6000 was preferred to PEG 2000 or 4000 as its binding to tannins was higher at near neutral pH values. The gas production increased with an increase in the amount of PEG 6000 up to 0.6 g/40 ml rumen-fluid-containing medium containing 0.5 g tannin-rich feed, beyond which no increase was observed. The percentage increase in gas value at 24 h fermentation correlated significantly with tannin values, the highest correlation (r 0.95) being with protein precipitation capacity of tannins. The increase in gas production was associated with higher production of short-chain fatty acids with little change in their molar proportions, suggesting an increase in organic matter digestibility by inclusion of the PEG in tannin-rich feeds. However, apparent and true digestibilities were lower on addition of the PEG, due to the presence of PEG-tannin complexes in the residues. The use of this bioassay (percentage increase in gas production in the presence of PEG 6000) along with other tannin assays would provide a better insight into the nutritional significance of tannins.