Comparative transcriptome analysis of different heat stress responses between self-root grafting line and heterogeneous grafting line in rose

Rose is sensitive to high temperature which will make the rose go into a semi-dormancy state.Grafting is an excellent way to enhance rose heat tolerance.Here,heat-tolerant Rosa multiflora‘Huanong Wuci 1'(W)and heat-sensitive Rosa chinensis‘Old Blush’(X)were selected as experimental materials.The RNA-seq technique was used to investigate the transcriptomes of self-root grafting line(XX0),heterogeneous grafting line(XW0),self-root grafting line under 6 h heat stress(XX6),and heterogeneous grafting line under 6 h heat stress(XW6).Under high temperature stress,multiple signaling pathways were activated,moreover,a large number of transcription factors and functional genes were induced,especially the HSFs and HSPs with remarkably upregulated expression levels.The GO analysis showed that the differences in the expressions of the genes related to fatty acids and carbohydrates were observed between self-root grafting line and heterogeneous grafting line.In addition,14 P450s were differentially expressed,and one lectin gene was up-regulated in XW0 vs XW6,but down-regulated in XX0 vs XX6.Considering physiological and biochemical traits such as relative electrolyte leakage,SOD activity,proline,and total soluble sugars,DEGs involved in these processes may be key factors to resist high temperature.The present study provides an insight into the complex mechanism underlying grafting in response to heat stress.Our results indicate that grafting is an effective way to improve rose heat resistance.

Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

The type 2 modified augmented design(MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline(http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

The Rice Processing Industry in Nepal: Constraints and Opportunities

A rice mill survey covering diverse rice processing companies in terms of their milling output, type of technology and year of establishment was conducted to understand the current situation of the rice milling industry and to identify enablers and barriers to its growth in Nepal. Coarse rice varieties dominate Nepal’s rice processing industry, with a 42% share by total weight, followed by medium rice (34%) and fine varieties (less than 7%). Polished white rice (Arwa) was the dominant rice type in Nepal in the survey, followed by parboiled and steamed rice. The price and profit margins increased from coarse to fine rice varieties and from Arwa to parboiled and steamed rice. The cost of milling also followed a similar trend. The rice milling industry in Nepal largely influences the adoption or non-adoption of any specific type of rice variety by dictating specific brands in the market and this has important implications for rice research and development. The rice processing industry of Nepal was unable to compete with the Indian rice milling industry because of: 1) low profit margins due to the high cost of rice production and procurement, 2) a lack of economies of scale, 3) a lack of milling technologies for long and extra-long and steamed rice in the country and a lack of investment to modernize rice milling technology, and 4) unavailability of paddy throughout the year locally. Millers were willing to upgrade their rice milling technology to include high throughput parboiling, steamed rice as well as long and extra-long grain rice. This will be a strategic decision in counteracting the ever-increasing rice imports in Nepal. We believe that the findings of the study will be vital for formulating an appropriate rice research, development and rice processing strategy for Nepal to achieve food and nutritional security and the Sustainable Development Goals.

Accuracy of genomic selection in biparental populations of flax(Linum usitatissimum L.)

Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection(GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS(rMP) and the efficiency of GS relative to phenotypic selection(RE) for three GS models: ridge regression best linear unbiased prediction(RR-BLUP),Bayesian LASSO(BL), and Bayesian ridge regression(BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rMPand RE, while BRR displayed a higher coefficient of determination(R^2)of the fitted models than did RR-BLUP or BL. The mean rMPand RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations.GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.

Changes in Inositol Phosphates in Low Phytic Acid Field Pea (<i>Pisum sativum</i>L.) Lines during Germination and in Response to Fertilization

Inositol phosphates are the main form of phosphorous (P) storage in legume seeds. Mutants low in inositol hexaphosphate (IP6), also known as phytic acid (PA), have been developed to increase iron (Fe) bioavailability and reduce P waste to the environment. The objectives of this study were to determine 1) inositol-P form changes during germination, and 2) the effect of P fertilizer application on seed PA, total P, and Fe concentration of three field pea (Pisum sativum L.) cultivars and two low-PA lines grown under greenhouse conditions. Low-PA field pea lines clearly had lower PA (1.3 - 1.4 mg·g-1) than cultivars (3.1 - 3.7 mg·g-1). Phytic acid concentration in both cultivars and low-PA lines decreased during germination, but tended to increase seven days after germination. Levels of inositol-3-phosphate-phosphate (IP3-P;0.6 mg·g-1) and inorganic P (1.8 - 2.0 mg·g-1) were higher in low-PA lines than in the field pea cultivars. Reduction of PA in low-PA line seeds may reduce seed Fe and total P concentrations, as levels in the low-PA lines (37 - 42 mg·kg-1 Fe;4003 - 4473 mg·kg-1 total P) were typically less than in field pea cultivars (37 - 55 mg·kg-1 Fe;3208 - 4985 mg·kg-1 total P) at different P fertilizer rates. Overall, IP3 is the major form of P present in low-PA field pea lines during germination;however IP6 is the major form of P present in field pea cultivars. Therefore, low-PA field pea lines could be a potential solution to increase Fe bioavailability, feed P utilization, and reduce P waste to the environment.

Influence of nitrogen sources on growth and mycotoxin production by isolates of Pyrenophora tritici-repentis from wheat

The fungus Pyrenophora tritici-repentis(Died.) Drechs. infects the leaves and kernels of wheat,causing tan spot and red smudge, respectively. Isolates of P. tritici-repentis have been reported to be both phytopathogenic and mycotoxigenic. This research investigates the influence of nitrogen sources on growth and production of mycotoxins by eight different isolates of P. tritici-repentis. A synthetic agar medium(SAM) was used with different nitrogen sources, both inorganic [(NH4Cl, NH4NO3and(NH4)2SO4)] and organic(L-alanine, L-histidine, and L-lysine), at a concentration of 37.5 mmol L-1. Individual isolates exhibited different growth rates that varied according to the nitrogen source added to the medium. The choice of nitrogen source also had a major effect on production of the mycotoxins emodin, catenarin and islandicin. The highest concentrations of emodin, 54.40 ± 4.46 μg g-1, 43.07 ± 23.39 μg g-1and28.91 ± 4.64 μg g-1of growth medium, were produced on the complex medium(V8-potato dextrose agar) by the isolates Alg-H2, 331-2 and TS93-71 B, respectively. A relatively high concentration of emodin also was produced by isolates Az35-5(28.29 ± 4.71 μg g-1of medium)and TS93-71B(27.03 ± 4.09 μg g-1of medium) on synthetic medium supplemented with L-alanine. The highest concentrations of catenarin(174.54 ± 14.46 μg g-1and 104.87 ±6.13 μg g-1of medium) were recorded for isolates TS93-71 B and Alg-H2 on synthetic medium supplemented with L-alanine and NH4 Cl, respectively. The highest concentration of islandicin(4.64 ± 0.36 μg g-1medium) was observed for isolate 331-2 in the presence of L-lysine. There was not a close relationship between mycelial growth and mycotoxin production by the fungal isolates. This is the first report on the influence of nitrogen sources on the production of mycotoxins by P. tritici-repentis.

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Gene cloning in repeat-rich polyploid genomes remains challenging.Here,we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene(R-gene)Pm69 derived from tetraploid wild emmer wheat.A conventional positional cloning approach was not effective owing to suppressed recombination.Chromosome sorting was compromised by insufficient purity.A Pm69 physical map,constructed by assembling Oxford Nanopore Technology(ONT)long-read genome sequences,revealed a rapidly evolving nucleotide-binding leucine-rich repeat(NLR)R-gene cluster with structural variations.A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing.Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel.Pm69 was successfully introgressed into cultivated wheat,and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada

Leptosphaeria maculans is a serious concern for canola production worldwide.For effective disease management,knowledge of the pathogen’s genetic variability and population structure is a prerequisite.In this study,whole-genome sequencing was performed for 162 of 1590 L.maculans isolates collected in the years 2007e2008 and 2012e2014 in Western Canada.DNA variants in genome-wide and specific regions including avirulence(Avr)genes were characterized.A total of 31,870 high-quality polymorphic DNA variants were used to study L.maculans genetic diversity and population structure.Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants.The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations.Principal component analysis with genome-wide variants showed that the isolates collected in 2012e2014 were more genetically diverse than those collected in 2007e2008.Population structure analysis discovered three distinct sub-populations.Although isolates from Saskatchewan and Alberta were of similar genetic composition,Manitoba isolates were highly diverse.Genome-wide association study detected DNA variants in genes AvrLm4-7,Lema_T86300,and Lema_T86310 associated with the years of collection.