Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches

‘Chinese Cling’is an important founder in peach breeding history due to the pleasant flavor.Genome-wide association studies(GWAS)combined with genomic selection are promising tools in fruit tree breeding,as there is a considerable time lapse between crossing and release of a cultivar.In this study,242 peaches from Shanghai germplasm were genotyped with 145456 single-nucleotide polymorphisms(SNPs).The six agronomic traits of fruit flesh color,fruit shape,fruit hairiness,flower type,pollen sterility,and soluble solids content,along with 14 key volatile odor compounds(VOCs),were recorded for multiple-statistical GWAS.Except the reported candidate genes,six novel genes were identified as associated with these traits.Thirty-nine significant SNPs were associated with eight VOCs.The putative candidate genes were confirmed for VOCs by RNA-seq,including three genes in the biosynthesis pathway found to be associated with linalool,soluble solids content,and cis-3-hexenyl acetate.Multiple-trait genomic prediction enhanced the predictive ability forγ-decalactone to 0.7415 compared with the single-trait model value of 0.1017.One PTS1-SSR marker was designed to predict the linalool content,and the favorable genotype 187/187 was confirmed,mainly existing in the‘Shanghai Shuimi’landrace.Overall,our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits.The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.

Analysis on Interaction Effects Between Variety and Site of Silage Maize Regional Test in Guizhou Province

Taking the yield in the second group of Guizhou silage maize regional test in 2019 as data information, 8 experimental sites and 12 silage maize varieties as experimental objects, the interaction effect between gene and environment was analyzed by using AMMI model. The results showed that the average fresh weight yield of each variety was 3 199.5~3 976.6 kg/667m^(2), among them, 5 varieties had an increase in the yield. Variety variation accounted for 10.51% of the total variation;experimental site variation accounted for 63.22% of the total variation;interaction effect variation between gene and environment accounted for 26.28% of the total variation;IPCA1 and IPCA2 variation accounted for 50.7% and 31.2% of the interaction variation, respectively;IPCA3 variation accounted for 7.25% of the interaction variation. g_4, g_8, g_9, g_10, g_11 and g_12 had better adaptability to e_1, e_2, e_6 and e_7;while g_1, g_2, g_3, g_5, g_6 and g_7 had better adaptability to e_3, e_4, e_5 and e_8. In consideration of yield, g_1(Huinongqing 2) and g_9(Xinyu 666) were silage maize varieties with high and stable yield;g_3(Hemuyu 905), g_8(Wuhuayu 3) and g_11(Liangdu 191) had general stability, and their yield was higher than that of the control;g_12(Jinduyu 999) had the worst stability and low yield.

Variation and Statistic Analysis of Agronomic Traits of Recombinant Inbred Lines of Brassica juncea L.

Correlation analysis and principal component analysis( PCA) were conducted for some agronomic traits of 139 recombinant inbred lines of Brassica juncea L. The results showed that under the environmental conditions in Guiyang,the flowering time,number of seeds per silique,plant height and thousand seed weight differed significantly among different lines. The results of principal component analysis showed that the lines could be classified into three groups. The results of Pearson correlation tests showed that the plant height was positively correlated with the flowering time( P < 0. 05),and the thousand seed weight was negatively correlated with the flowering time and number of seeds per silique( P < 0. 01).

Identification of functional tumor necrosis factor-alpha promoter variants associated with Helicobacter pylori infection in the Sudanese population: Computational approach

BACKGROUND Helicobacter pylori(H.pylori)is a ubiquitous bacterium that affects nearly half of the world’s population with a high morbidity and mortality rate.Polymorphisms within the tumor necrosis factor-alpha(TNF-A)promoter region are considered a possible genetic basis for this disease.AIM To functionally characterize the genetic variations in the TNF-A 5’-region(-584 to+107)of Sudanese patients infected with H.pylori using in silico tools.METHODS An observational study was carried out in major public and private hospitals in Khartoum state.A total of 122 gastric biopsies were taken from patients who had been referred for endoscopy.Genomic DNA was extracted.Genotyping of the TNF-A-1030 polymorphism was performed using PCR with confronting two-pair primer to investigate its association with the susceptibility to H.pylori infection in the Sudanese population.Furthermore,Sanger sequencing was applied to detect single nucleotide polymorphisms in the 5’-region(-584 to+107)of TNF-A in H.pylori-infected patients.Bioinformatics analyses were used to predict whether these mutations would alter transcription factor binding sites or composite regulatory elements in this region.A comparative profiling analysis was conducted in 11 species using the ECR browser and multiple-sequence local alignment and visualization search engine to investigate the possible conservation.Also,a multivariate logistic regression model was constructed to estimate odds ratios and their 95%confidence intervals for the association between TNF-A-1030,sociodemographic characteristics and H.pylori infection.Differences were statistically significant if P<0.05.Statistical analyses were performed using Stata version 11 software.RESULTS A total of seven single nucleotide polymorphisms were observed in the TNF-A 5’-region of Sudanese patients infected with H.pylori.Only one of them(T>A,-76)was located at the in silico-predicted promoter region(-146 to+10),and it was predicted to alter transcription factor binding sites and composite regulatory elements.A novel mutation(A>T,+27)was detected in the 5’untranslated region,and it could affect the post-transcriptional regulatory pathways.Genotyping of TNF-A-1030 showed a lack of significant association between-1030T and susceptibility to H.pylori and gastric cancer in the studied population(P=0.1756)and(P=0.8116),respectively.However,a significant association was detected between T/C genotype and H.pylori infection(39.34%vs 19.67%,odds ratio=2.69,95%confidence interval:1.17-6.17,P=0.020).Mammalian conservation was observed for the(-146 to+10)region in chimpanzee(99.4%),rhesus monkey(95.6%),cow(91.8%),domesticated dog(89.3%),mouse(84.3%),rat(82.4%)and opossum(78%).CONCLUSION Computational analysis was a valuable method for understanding TNF-A gene expression patterns and guiding further in vitro and in vivo experimental validation.

Plant-pollinator metanetworks in fragmented landscapes:a simulation study

Background The topology of the plant-pollinator network can be explained by the species’abundance and their random interactions.Plant-pollinator networks can be studied in the context of a landscape,because each patch can accommodate a certain local network.Local populations of pollinators in the landscape can be connected through migration and then constitute a metanetwork that is known as a combination of spatial and ecological networks.In this regard,habitat fragmentation can affect the topology of plant-pollinator metanetworks through changes in the species abundance and limiting their interactions.However,it is not clear what pattern(fragmented or aggregated)of the landscape structure can accommodate networks with a higher degree of specialization.Methods we created simulated landscapes with different forest proportions scenarios(from 5%to 50%of the total landscape)and degrees of fragmentation.Then,for each landscape,we limited the proportion of pollinators to the forest patch.We assumed that plants and pollinators are randomly distributed around the landscape and interact randomly.We used landscape metrics to measure different aspects of landscape structure and bipartite metrics for calculating the degree of specialization in plant-pollinator networks.Results The statistical relationship between bipartite and landscape metrics showed that the relationship between the topology of plant-pollinator networks and the landscape structure is affected by the forest amount in the landscape and the degree of forest fragmentation.We also found that according to the nestedness and H2(a measure of specialization)metrics,fragmented landscapes contain more general plant-pollinator networks.Conclusions Our findings suggest that fragmented landscapes,characterized by scattered forest patches,can promote higher levels of interaction between limited pollinators and diverse flowers,leading to more general plant-pollinator networks.

Effects of rhizobacteria Paenibacillus polymyxa APEC136 and Bacillus subtilis APEC170 on biocontrol of postharvest pathogens of apple fruits

In this study, plant growth-promoting rhizobacteria（PGPR） were evaluated as potential biocontrol agents against postharvest pathogens of apple fruits. In vitro bioassays revealed that, out of 30 isolates screened, isolates APEC136 and APEC170 had the most significant inhibitory effects against the mycelial growth of several fungal pathogens. Analysis of 16 S ribosomal RNA（rR NA） sequences identified the two effective isolates as Paenibacillus polymyxa and Bacillus subtilis, respectively. The two strains showed greater growth in brain-heart infusion broth than in other growth media. Treatment of harvested apples with suspensions of either strain reduced the symptoms of anthracnose disease caused by two fungal pathogens, Colletotrichum gloeosporioides and Colletotrichum acutatum, and white rot disease caused by Botryosphaeria dothidea. Increased productions of amylase and protease by APEC136, and increased productions of chitinase, amylase, and protease by APEC170 might have been responsible for inhibiting mycelial growth. The isolates caused a greater reduction in the growth of white rot than of anthracnose. These results indicate that the isolates APEC136 and APEC170 are promising agents for the biocontrol of anthracnose and white rot diseases in apples after harvest, and suggest that these isolates may be useful in controlling these diseases under field conditions.