Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.)

Genome-wide association study(GWAS)is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species.In this study,we conducted GWAS to explore quantitative trait loci(QTL)for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds.The eight traits included fruit weight,fruit width,fruit height,fruit shape index,pericarp thickness,locule number,fruit firmness,and brix.Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years.We filtered 34,550 confident SNPs from the 51K Axiom®tomato array based on<10%of missing data and>5%of minor allele frequency for association analysis.The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix.To identify marker-trait associations(MTAs),four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model(MLMM).A total of 30 significant MTAs was detected over data sets for eight fruit traits at P<0.0005.The number of MTA per trait ranged from one(brix)to seven(fruit weight and fruit width).Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits,suggesting pleiotropic effects of QTL.Furthermore,16 of 30 MTAs suggest potential novel QTL for eight fruit traits.These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.

Genome-wide SNP discovery and core marker sets for assessment of genetic variations in cultivated pumpkin(Cucurbita spp.)

Three pumpkin species Cucurbita maxima,C.moschata,and C.pepo are commonly cultivated worldwide.To identify genome-wide SNPs in these cultivated pumpkin species,we collected 48 F1 cultivars consisting of 40 intraspecific hybrids(15 C.maxima,18 C.moschata,and 7 C.pepo)and 8 interspecific hybrids(C.maxima x C.moschata).Genotyping by sequencing identified a total of 37,869 confident SNPs in this collection.These SNPs were filtered to generate a subset of 400 SNPs based on polymorphism and genome distribution.Of the 400 SNPs,288 were used to genotype an additional 188 accessions(94 F1 cultivars,50 breeding lines,and 44 landraces)with a SNP array-based platform.Reliable polymorphisms were observed in 224 SNPs(78.0%)and were used to assess genetic variations between and within the four predefined populations in 223 cultivated pumpkin accessions.Both principal component analysis and UPGMA clustering found four major clusters representing three pumpkin species and interspecific hybrids.This genetic differentiation was supported by pairwise Fst and Nei’s genetic distance.The interspecific hybrids showed a higher level of genetic diversity relative to the other three populations.Of the 224 SNPs,five subsets of 192,96,48,24,and 12 markers were evaluated for variety identification.The 192,96,and 48 marker sets identified 204(91.5%),190(85.2%),and 141(63.2%)of the 223 accessions,respectively,while other subsets showed<25%of variety identification rates.These SNP markers provide a molecular tool with many applications for genetics and breeding in cultivated pumpkin.

Nucleus-Encoded Thylakoid Protein,OsY3IP1,Confers Enhanced Tolerance to Saline and Alkaline Stresses in Rice

Abiotic stress confers serious damage to the photosynthetic machinery,often resulting in plant growth inhibition.Hypothetical chloroplast open reading frame 3(Ycf3)-interacting protein 1(Y3IP1)is a nucleus-encoded thylakoid protein and plays an essential role in the assembly of photosystem I.The full-length cDNA over-expresser(FOX)gene-hunting system is an approach using systemically generated gain-of-function mutants.Among the FOX-rice lines,a line CE175 overexpressing rice Y3IP1gene(Os Y3IP1)displayed less inhibition of root growth under saline(NaCl)stress.The expression of Os Y3IP1 was up-regulated under saline and alkaline(Na2CO3)stresses in the rice variety Kitaake.After saline and alkaline treatments,transgenic Kitaake overexpressing OsY3IP1-GFP(OsY3IP1-GFPox/Kit)displayed higher levels of chlorophyll content compared to Kitaake.Under the stress conditions,the maximum quantum yield of photosystem II photochemistry levels was higher in OsY3IP1-GFPox/Kit than in Kitaake.The increased tolerance conferred by OsY3IP1 overexpression correlated with reduced reactive oxygen species accumulation.Our data provide new insights into the possible role of OsY3IP1 in the pathway suppressing photooxidative damage under stress conditions.These features can be further exploited to improve saline and alkaline tolerances of rice plants in future.

Indigenous parasitoids as effective natural enemies of Phyllocnistis citrella(Lepidoptera:Gracillariidae)in Korea

This study is aimed to investigate the occurrence of Phyllocnistis citrella Stainton （citrus leafminer; CLM）, which has recently caused increasing damage to citrus farms in southern South Korea, and its natural enemies, which can act as biological control agents. In the present study, CLM monitoring using sex pheromone traps were conducted in the major citrus farms in the Jeju region in South Korea. Also a survey of parasites was carried out to detect the effective control agent for CLM. During the investigation from 2011 to 2015, a relatively large number of adult CLM （2,386,990） were observed in the sex pheromone traps. The mean annual occurrence of CLM was 477,398, which showed an increasing trend with the increase in temperature. A survey of parasites was conducted in November 2015. Six parasites were found, of which, Quadrastichus sp. and Sympiesis sp. showed the highest rates of parasitism. The mean rate of parasitism during the survey period was 3.97 %. We discovered four new species of parasites of CLM in South Korea.