World Vegetable Center

About: World Vegetable Center is a nonprofit organization based out in Tainan City, Taiwan. It is known for research contribution in the topics: Population & Agriculture. The organization has 294 authors who have published 364 publications receiving 8785 citations. The organization is also known as: AVRDC, Asian Vegetable Research and Development Center.

Application of Cytochrome Oxidase I Sequences for Phylogenetic Analysis and Identification of Thrips Species Occurring on Vegetable Crops

Abstract: Thrips are direct pests as well as vectors of important viruses infecting crop plants. One of the major constraints in studying the relationship between thrips vectors and tospoviruses is the difficulty of identifying the vector species because of high intraspecific variation among thrips populations. Molecular approaches have been used to identify species differences. In this study, partial cytochrome oxidase I (COI) sequences were used to understand the phylogenetic relationship among thrips populations, and assess their usefulness to identify and classify unknown thrips species collected from different crops. In total, 29 COI variants were obtained while examining the sequence polymorphisms in COI of 182 insects analyzed in this study, which were collected from six countries on tomato, chilli, onion, cabbage, cucumber, watermelon, Ethiopian mustard, French bean, and peanut. The phylogenetic analysis showed that the insects used in this study clustered with five distinct species-groups designated as Thrips palmi group, T. tabaci group, Frankliniella occidentalis group, Scirtothrips dorsalis group and an unclassified group. Higher intraspecific genetic variation was observed in S. dorsalis and T. palmi followed by T. tabaci and F. occidentalis. Thus, it was confirmed that the COI gene could be useful in grouping different thrips species and genera that coexist in a particular cropping system.

Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6

Abstract: Simple sequence repeat motifs are abundant in plant genomes and are commonly used molecular markers in plant breeding. In tomato, currently available genetic maps possess a limited number of simple sequence repeat (SSR) markers that are not evenly distributed in the genome. This situation warrants the need for more SSRs in genomic regions lacking adequate markers. The objective of the study was to develop SSR markers pertaining to chromosome 6 from bacterial artificial chromosome (BAC) sequences available at Solanaceae Genomics Network. A total of 54 SSR primer pairs from 17 BAC clones on chromosome 6 were designed and validated. Polymorphism of these loci was evaluated in a panel of 16 genotypes comprising of Solanum lycopersicum and its wild relatives. Genetic diversity analysis based on these markers could distinguish genotypes at species level. Twenty-one SSR markers derived from 13 BAC clones were polymorphic between two closely related tomato accessions, West Virginia 700 and Hawaii 7996 and were mapped using a recombinant inbred line population derived from a cross between these two accessions. The markers were distributed throughout the chromosome spanning a total length of 117.6 cM following the order of the original BAC clones. A major QTL associated with resistance to bacterial wilt was mapped on chromosome 6 at similar location of the reported Bwr-6 locus. These chromosome 6-specific SSR markers developed in this study are useful tools for cultivar identification, genetic diversity analysis and genetic mapping in tomato.

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome

Abstract: We performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ssp. sublobata TC1966, V. radiata var. radiata NM92 and the recombinant inbred line RIL59 derived from a cross between TC1966 and NM92. Moreover, we performed deep sequencing of the RIL59 transcriptome to investigate transcript variability. The mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. A total of 213 simple sequence repeats were identified in the chloroplast genomes of NM92 and RIL59; 78 single nucleotide variants and nine indels were discovered in comparing the chloroplast genomes of TC1966 and NM92. Analysis of the mungbean chloroplast transcriptome revealed mRNAs that were affected by transcriptional slippage and RNA editing. Transcriptional slippage frequency was positively correlated with the length of simple sequence repeats of the mungbean chloroplast genome (R2=0.9911). In total, 41 C-to-U editing sites were found in 23 chloroplast genes and in one intergenic spacer. No editing site that swapped U to C was found. A combination of bioinformatics and experimental methods revealed that the plastid-encoded RNA polymerase-transcribed genes psbF and ndhA are affected by transcriptional slippage in mungbean and in main lineages of land plants, including three dicots (Glycine max, Brassica rapa, and Nicotiana tabacum), two monocots (Oryza sativa and Zea mays), two gymnosperms (Pinus taeda and Ginkgo biloba) and one moss (Physcomitrella patens). Transcript analysis of the rps2 gene showed that transcriptional slippage could affect transcripts at single sequence repeat regions with poly-A runs. It showed that transcriptional slippage together with incomplete RNA editing may cause sequence diversity of transcripts in chloroplasts of land plants.

Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium).

Abstract: Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.

Yield and quality of two tomato (Solanum lycopersicum L.) cultivars as influenced by drip and furrow irrigation using waters having high residual sodium carbonate

Abstract: Performance of tomato when irrigated with sodic waters particularly under drip irrigation is not well known. A Weld experiment was conducted for 3 years to study the response of tomato crop to sodic water irrigation on a sandy loam soil. Irrigation waters having 0, 5 and 10 mmol c L i1 residual sodium carbonate (RSC) were applied through drip and furrow irrigation to two tomato cultivars, Edkawi (a salt tolerant cultivar) and Punjab Chhuhara (PC). High RSC of irrigation water signiWcantly increased soil pH, ECe and exchangeable sodium percent- age progressively; the increases were higher in furrow com- pared to drip irrigation. EVect of high RSC on increasing bulk density and decreasing inWltration rate of soil was also pronounced in furrow-irrigated plots. Higher soil moisture and lower salinity near the plant was maintained under drip irrigation than under furrow irrigation. Performance of the two cultivars was signiWcantly diVerent; pooled over 2002- 03 and 2003-04 seasons, PC yielded 38.8 and 30.0 Mg ha i1 and Edkawi yielded 31.8 and 22.9 Mg ha i1 under drip and furrow irrigation, respectively. At RSC10, cultivar PC pro- duced 38 and 46% higher fruit yield than cultivar Edkawi under drip and furrow irrigation, respectively. Reduction in fruit yield at higher RSC was due to lower fruit weight under drip irrigation and due to reduced fruit number as well as fruit weight under furrow irrigation. Decrease in fruit weight was more pronounced in cultivar Edkawi than in cultivar PC. Increase in RSC lowered quality of the fruits except the ascorbic acid content. High RSC under drip irri- gation, in general, had lesser deteriorating eVect on the fruit quality particularly for cultivar PC than under furrow irri- gation. For obtaining high tomato yield and better-quality fruits using high RSC sodic waters, drip irrigation should be preferred over furrow irrigation. Better performance of local cultivar PC compared to Edkawi at medium and high RSC suggests that cultivars categorized as tolerant to salin- ity should be evaluated in the sodic environment particu- larly when irrigated with high RSC sodic waters.