Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

Effects of the nitrification inhibitor nitrapyrin and the plant growth regulator gibberellic acid on yield-scale nitrous oxide emission in maize fields under hot climatic conditions

Nitrification inhibitors are widely used in agriculture to mitigate nitrous oxide(N_(2)O)emission and increase crop yield.However,no concrete information on their mitigation of N_(2)O emission is available under soil and environmental conditions as in Pakistan.A field experiment was established using a silt clay loam soil from Peshawar,Pakistan,to study the effect of urea applied in combination with a nitrification inhibitor,nitrapyrin(2-chloro-6-tri-chloromethyl pyridine),and/or a plant growth regulator,gibberellic acid(GA_3),on N_(2)O emission and the nitrogen(N)uptake efficiency of maize.The experimental design was a randomized complete block with five treatments in four replicates:control with no N(CK),urea(200 kg N ha^(-1))alone,urea in combination with nitrapyrin(700 g ha^(-1)),urea in combination with GA_3(60 g ha^(-1)),and urea in combination with nitrapyrin and GA_3.The N_(2)O emission,yield,N response efficiency,and total N uptake were measured during the experimental period.The treatment with urea and nitrapyrin reduced total N_(2)O emission by 39%–43%and decreased yield-scaled N_(2)O emission by 47%–52%,relative to the treatment with urea alone.The maize plant biomass,grain yield,and total N uptake increased significantly by 23%,17%,and 15%,respectively,in the treatment with urea and nitrapyrin,relative to the treatment with urea alone,which was possibly due to N saving,lower N loss,and increased N uptake in the form of ammonium;they were further enhanced in the treatment with urea,nitrapyrin,and GA_3 by 27%,36%,and 25%,respectively,probably because of the stimulating effect of GA_3 on plant growth and development and the reduction in biotic and abiotic stresses.These results suggest that applying urea in combination with nitrapyrin and GA_3 has the potential to mitigate N_(2)O emission,improve N response efficiency,and increase maize yield.

Compatibility of early natural enemy introductions in commercial pepper and tomato greenhouses with repeated pesticide applications

Successful integrated pest management in protected crops implies an evalu-ation of the compatibility of pesticides and natural enemies(NE),as control strategies that only rely on one tactic can fail when pest populations exceed NE activity or pests become resistant to pesticides.Nowadays in Almeria(Spain),growers release NE prior to transplanting or early in the crop cycle to favor their settlement before pest arrival because this improves biocontrol efficacy,although it extends pesticide exposure periods.The pur-pose of this research was to evaluate the compatibility of two applications of pesticides with key NE in 2-year trials inside tomato and sweet pepper commercial greenhouses:Nesidiocoris tenuis(Reuter)(Hemiptera:Miridae),Orius laevigatus(Say)(Hemiptera:Anthocoridae)and Amblyseius swirskii(Athias-Henriot)(Acari:Phytoseidac).In tomato,flubendiamide and chlorantraniliprole(IOBC category 1)were compatible with N.tenuis,but chlorpyrifos.:methyl and spinosad(IOBC categories 2-3),which efectively reduced Tiuta absoluta(Meyrick)(Lepidoptera:Gelechidae)density,compromised its predatory activity.In sweet pepper,chlorantraniliprole(IOBC category 1)was the only pesticide compatible with O.laevigatus while chlorantraniliprole,emamectin benzoate,spirote-tramat and pymetrozine were harmless(IOBC category 1)to Amblyseius swirskii,and sulfoxaflor slightly harmful(IOBC category 2)to this phytoseiid predator.

Nitrification inhibitor nitrapyrin does not affect yield-scaled nitrous oxide emissions in a tropical grassland

Urea is the most common nitrogen(N)fertilizer used in the tropics but it has the risk of high gaseous nitrogen(N)losses.Use of nitrification inhibitor has been suggested as a potential mitigation measure for gaseous N losses in N fertilizer-applied fields.In a field trial on a tropical Andosol pastureland in Costa Rica,gaseous emissions of ammonia(NH_(3))and nitrous oxide(N_(2)O)and grass yield were quantified from plots treated with urea(U;41.7 kg N ha^(-1)application^(-1))and urea plus the nitrification inhibitor nitrapyrin(U+NI;41.7 kg N ha^(-1)application^(-1)and 350 g of nitrapyrin for each 100 kg of N applied)and control plots(without U and NI)over a six-month period(rainy season).Volatilization of NH_(3)(August to November)in U(7.4%±1.3%of N applied)and U+NI(8.1%±0.9%of N applied)were not significantly different(P>0.05).Emissions of N_(2)O in U and U+NI from June to November were significantly different(P<0.05)only in October,when N_(2)O emission in U+NI was higher than that in U.Yield and crude protein production of grass were significantly higher(P<0.05)in U and U+NI than in the control plots,but they were not significantly different between U and U+NI.There was no significant difference in yield-scaled N_(2)O emission between U(0.31±0.10 g N kg^(-1)dry matter)and U+NI(0.47±0.10 g N kg^(-1)dry matter).The results suggest that nitrapyrin is not a viable mitigation option for gaseous N losses under typical N fertilizer application practices of pasturelands at the study site.