Research Interests: Biology and Crop Science
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Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both... more
Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks...
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The objective of this study was to examine the relative impact of genetics and environment on phenolic and carotenoid profiles in peach (Prunus persica) germplasm. Fully mature, (“ready-to-eat” stage) firm fruit of peach cultivars China... more
The objective of this study was to examine the relative impact of genetics and environment on phenolic and carotenoid profiles in peach (Prunus persica) germplasm. Fully mature, (“ready-to-eat” stage) firm fruit of peach cultivars China Pearl, Contender, and Carolina Gold were collected from established trees at two North Carolina locations in 2009 and 2010. Advanced breeding selections NC Yellow and NC 97-48 were collected from a single location in both years. Using tandem extractions and chromatography analyses, 10 carotenoids and 24 phenolic compounds were quantified separately in the peel and flesh. Statistically significant differences were noted among peach cultivars and advanced selections for β-carotene, cyanidin-3-glucoside, cyanidin-3-rutinoside, cholorogenic acid, quercetin-3-glucoside, and individual procyanidins. Peel anthocyanin (ANC) concentration ranged from 183 mg/100 g in ‘Contender’ to non-detectable levels in NC97-48 and NC Yellow. ‘China Pearl’ and ‘Carolina Gol...
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Yugoslavia has a diverse population of vineyard peaches, which has been rarely used for genetic improvement. A programme for characterising the diversity of vineyard peaches began at Novi Sad in 1989 and some 457 vineyard peach accessions... more
Yugoslavia has a diverse population of vineyard peaches, which has been rarely used for genetic improvement. A programme for characterising the diversity of vineyard peaches began at Novi Sad in 1989 and some 457 vineyard peach accessions have been collected and evaluated for morphological and phenological traits. To assess the molecular diversity of the vineyard peaches collected in comparison with standard cultivars, we used isoenzymes and RFLPs. We analysed 79 vineyard peach accessions and 33 peach cultivars for 32 enzyme systems using PAGE. Good activity and separation were achieved for all systems including ones previously reported as poorly resolved. On the basis of polymorphism observed for 21 enzyme systems (ACP, AKP, AMY, ADH, CAD, DIA, EST, FRK, GAL, GLU, GOT, GDH, HEX, IDH, MDH, ME, MNR, PEP, PRX, PHO and SKD) 31 loci were scored in vineyard peach and cultivars. For 11 enzyme systems (ACO, AAP, ARA, ENP, FDH, GPI, G6PDH, G3PDH, LAP, PGM and PGD) no polymorphism was revealed. Thirty-six vineyard peaches and 16 cultivars that revealed high levels of heterozygosity were analysed by RFLPs. Almond, peach and cherry probes from the European Prunus Mapping Project were used in combination with the restriction endonucleases Dra I, Eco RI and Hind III. Polymorphism was revealed with 9 probes and 14 loci were proposed. Vineyard peach accessions were polymorphic for 14 loci, and cultivars for 11.
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ABSTRACT
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Red skin pigmentation develops through the flavonoid and anthocyanin pathways. Both genetic and environmental stimuli and their interaction (genotype x environment) control the regulation of this pathway. Sunlight induces the progression... more
Red skin pigmentation develops through the flavonoid and anthocyanin pathways. Both genetic and environmental stimuli and their interaction (genotype x environment) control the regulation of this pathway. Sunlight induces the progression of red skin development. To study the genetic control of red skin pigmentation or blush in peach a controlled cross between two cultivars with contrasting phenotypes, ‘Zin Dai’ (~30% red skin) and ‘Crimson Lady’ (~100% red skin), was made. One F1 hybrid, BY02p4019, with intermediate levels of blush (~65% red) was selfed to generate a segregating F2 blush population (ZC2). The segregating population was phenotyped for blush for four years (2007, 2008, 2010, 2011) using a visual rating scale (0–5) and in 2011 using a colorimeter (L*, a*, b*). Twenty-five individuals, exhibiting a blush range from 0 (0% red) to 5 (100% red) and a normal distribution for this trait, were genotyped with an IPSC 9K peach SNP array v1. A ZC2 genetic linkage map was constru...
We used genotyping by sequencing (GBS), a low-cost, high-throughput sequencing technology to genotype 333 Prunus accessions, preserved at the Prunus collection of the National Clonal Germplasm Repository (NCGR) in Davis, California. The... more
We used genotyping by sequencing (GBS), a low-cost, high-throughput sequencing technology to genotype 333 Prunus accessions, preserved at the Prunus collection of the National Clonal Germplasm Repository (NCGR) in Davis, California. The Prunus collection is the second largest in this genebank with more than 90 taxa and in excess of 1600 accessions of Prunus spp that includes almonds, apricots, cherries, peaches and plums. The accessions genotyped here consist of heirlooms (old cultivars never patented, or off patent), landraces, breeder’s lines, and wild relatives of the peach from all over the world. Majority of accessions belonged to Prunus persica (84%), with 10% of them being wild relatives (P. mira, P. davidiana, and P. ferganensis) and 6% categorized as hybrids between peach and other related species and Prunus spp. The method produced on average 1 million sequence reads per accession, with majority of the accessions having more than 500,000 reads. We identified 18,008 single-...
New cultivar development for peach in the U.S. can be divided into two types according to usage of fruit: fresh market and processing market. Objectives common to all peach breeding programs include improving and maintaining fruit quality... more
New cultivar development for peach in the U.S. can be divided into two types according to usage of fruit: fresh market and processing market. Objectives common to all peach breeding programs include improving and maintaining fruit quality (flavor, firmness, and appearance), productivity, size, and season extension. These trait targets are complemented with emphases on ease of processing, disease and pest resistance, a greater diversity of fruit types, and adaptation to low-chill zones in individual programs. Genetic markers associated with some of these traits are available and useful for informing crossing decisions and seedling selection decisions. Despite being one of the best characterized Rosaceae crops with genomic resources including a whole genome sequence, a reference genetic map, EST libraries, and a growing list of marker-locus-trait associations, application of these resources in peach breeding efforts is still limited. The RosBREED project (www.rosbreed.org) aims to bri...
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Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for the adoption of marker-assisted breeding. Peach serves as a well resourced model fruit crop while cherry stands to directly benefit from... more
Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for the adoption of marker-assisted breeding. Peach serves as a well resourced model fruit crop while cherry stands to directly benefit from research advances in its relative. Three “jewels in the genome” for peach and cherry are the current targets for application in breeding. Peach breeders select cultivar candidates that meet their criteria for fruit texture (melting vs. non-melting flesh) and pit adherence to the flesh (clingstone vs. freestone). These phenotypes are explained by genes at the Freestone-Melting flesh locus on peach chromosome 4 that contains the endoPG gene (a gene encoding a cell wall pectin-cleaving enzyme called endopolygalactouronase that plays a major role in fruit softening). Genetic tests are available for the functional alleles that can be used to predict whether peach fruit will be freestone melting flesh (FMF), clingstone melting flesh (CMF), clingstone non-mel...
ABSTRACT Temperature and water availability are significant factors driving the evolution of abiotic stress tolerance in plants through natural selection. Levels of both freezing and drought tolerance can vary widely between and within... more
ABSTRACT Temperature and water availability are significant factors driving the evolution of abiotic stress tolerance in plants through natural selection. Levels of both freezing and drought tolerance can vary widely between and within species. A common feature among studies of drought- and cold-induced gene expression has been an increase in the abundance of dehydrins, a sub-group of late-embryogenesis-abundant (LEA) genes. Using the recently released peach genome sequence, we have identified five ‘signature’ dehydrin genes and their promoters. While dehydrins encoded by PpDhn1-3 have been previously described, two additional deydrins in our study, PpDhn4 and PpDhn5, have not been previously characterized. Using the genome sequence data, we compared the amino acid sequence similarities of the conceptually translated protein products of this gene family, as well as similarities among the promoters of the individual genes. To identify which paralogs might be useful in breeding programs to improve cold hardiness, we assessed the expression of the dehydrin gene family in bark tissues sampled from five named cultivars in the winter and summer of 2010 (Clemson, SC). Results from qRT-PCR analysis indicated considerable diversity in dehydrin gene expression between cultivars and between different dehydrin paralogs.
ABSTRACT Red skin coloration, or blush, is an important trait for fresh market peaches. High red skin coloration is appealing to the consumer’s eye and the anthocyanin compound associated with blush provides flavor and nutrients important... more
ABSTRACT Red skin coloration, or blush, is an important trait for fresh market peaches. High red skin coloration is appealing to the consumer’s eye and the anthocyanin compound associated with blush provides flavor and nutrients important in the daily human diet. Blush is quantitatively inherited and presents practical challenges in selection. Nonetheless, traditional breeding has been successful in developing peach cultivars with increased levels of blush; though traditional breeding is time consuming with at least 15 years before a new cultivar release. Therefore, to overcome the limitations of traditional breeding and ensure development of high blush peach cultivars, application of molecular marker(s) associated with blush development via marker-assisted selection (MAS) was evaluated. Previous research reported a major QTL locus, Blush.Pp.ZC-3.1, associated with blush in peach. Two single nucleotide polymorphism (SNP) markers, flanking blush QTL, SNP_IGA_341962 and SNP_3_12878608, were converted into Cleaved Amplified Polymorphic Sequence (CAPS) markers, and evaluated for their MAS potential in peach. A high blush genotype (AA or TG) was observed in 82 and 62% of analyzed material, confirming the tendency of modern peach breeding programs to develop high blushed cultivars. Application of these markers in a fresh market peach breeding program will enable parental selection to ensure a majority of progeny with the desired phenotype, and seedling selection to suggest which progeny to keep for further evaluation.
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ABSTRACT Recent advances in genomic sequencing technology have allowed the addition of a number of crops to the growing list of completely sequenced genomes. We have analyzed the peach (Prunus persica [L] Batsch) genome of a doubled... more
ABSTRACT Recent advances in genomic sequencing technology have allowed the addition of a number of crops to the growing list of completely sequenced genomes. We have analyzed the peach (Prunus persica [L] Batsch) genome of a doubled haploid line (&#39;Lovell 2D&#39;) for the dehydrin gene family and compared its members to the genomes of Arabidopsis, poplar, apple and rice. This comparison suggests that peach has about half the complement of dehydrin genes found in the other genomes surveyed. Whereas Arabidopsis has 10 genes encoding bona fide dehydrins, and poplar, apple and rice all have nine dehydrin homologs, peach has only five, identified on the basis of signature sequences, i.e. the K domain, and conserved regions, e.g. the Y domain and the serine tract. Expression analysis of the peach dehydrin genes compared to those in rice and Arabidopsis indicates that some functions have been preserved between peach dehydrins and their homologs from other species, while other peach dehydrins have evolved to fill overlapping roles in response to abiotic stress exposure.
Although rose transformation is successful, it remains difficult to transform myriad rose species as well as different rose genotypes. In this protocol, a detailed description of rose transformation is presented. This protocol relied on... more
Although rose transformation is successful, it remains difficult to transform myriad rose species as well as different rose genotypes. In this protocol, a detailed description of rose transformation is presented. This protocol relied on Agrobacterium-mediated transfer of embryogenic callus cultures. There are many critical steps that must be followed to achieve successful transformation; however, it is important to keep in mind that these apply to a selected number of genotypes, and as a different genotype is subjected to transformation, modifications of this protocol must be made to achieve successful transformation.
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All economically important Brassica species have been successfully transformed using Agrobacterium tumefaciens. Although different tissues have been used as explants, hypocotyls remain the most desirable explants for Brassica tissue... more
All economically important Brassica species have been successfully transformed using Agrobacterium tumefaciens. Although different tissues have been used as explants, hypocotyls remain the most desirable explants for Brassica tissue culture owing to their amenability to regeneration. Young explants excised from 3- to 4-d-old seedlings have exhibited optimal regeneration potential; the addition of adjuvants such as silver nitrate to the selection medium is necessary to achieve high efficiency of transformation. This chapter describes an Agrobacterium-mediated transformation protocol for Indian mustard based on inoculation of hypocotyls. The selectable marker gene used encodes for neomycin phosphotransferase II (nptII), and the selection agent is kanamycin.
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Research Interests: Engineering, Genetics, Physics, Chemistry, Biology, and 15 moreBreeding, International Cooperation, Medicine, Multidisciplinary, Next generation sequencing, Marker assisted selection, Genetic Map, Germplasm, Empirical Evaluation, Genotyping, Genetic Architecture, Genetic Relatedness, Genetic Markers, Detection Algorithm, and Gene frequency
Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is a serious disease of swine and contributes to severe worldwide economic losses in swine production. Current vaccines against PRRS rely on the use... more
Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is a serious disease of swine and contributes to severe worldwide economic losses in swine production. Current vaccines against PRRS rely on the use of an attenuated-live virus; however, these are unreliable. Thus, alternative effective vaccines against PRRS are needed. Plant-based subunit vaccines offer viable, safe, and environmentally friendly alternatives to conventional vaccines. In this study, efforts have been undertaken to develop a soybean-based vaccine against PRRSV. A construct carrying a synthesized PRRSV-ORF7 antigen, nucleocapsid N protein of PRRSV, has been introduced into soybean, Glycine max (L.) Merrill. cvs. Jack and Kunitz, using Agrobacterium-mediated transformation. Transgenic plants carrying the sORF7 transgene have been successfully generated. Molecular analyses of T(0) plants confirmed integration of the transgene and transcription of the PRRSV-ORF7. Presence of a 15-kDa protein in seeds of T(1) transgenic lines was confirmed by Western blot analysis using PRRSV-ORF7 antisera. The amount of the antigenic protein accumulating in seeds of these transgenic lines was up to 0.65% of the total soluble protein (TSP). A significant induction of a specific immune response, both humoral and mucosal, against PRRSV-ORF7 was observed following intragastric immunization of BALB/c female mice with transgenic soybean seeds. These findings provide a &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;proof of concept&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;, and serve as a critical step in the development of a subunit plant-based vaccine against PRRS.
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Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns.... more
Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern blots, there are two copies of SbeII genes in the apple genome. Comparisons of genomic sequences between monocots and eudicots have revealed that the genomic structure of SbeII genes is conserved. However, the 5&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-terminal region of coding DNA sequences of SbeII genes shows greater divergence than the 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-terminal region between monocots and eudicots. Phylogenetic analysis of DNA sequences has demonstrated that the duplication patterns of SbeII genes are different between monocots and eudicots. In monocots, the duplication of SbeII genes must have occurred prior to the radiation of grasses (Poaceae); while, in eudicots, the expansion of SbeII genes must have followed the process of speciation.
Research Interests: Genetics, Genomics, Biology, Medicine, Phylogenetic analysis, and 15 moreGenome, Gene, Gene Duplication, Biological evolution, Gen, Malus, Genome Comparison, Genomic DNA, Glycosyltransferases, Genome sequence, Amino Acid Sequence, Base Sequence, Gene expression profiling, DNA sequence, and Expression pattern
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... KSENIJA GASIC1, ALVARO HERNANDEZ2 and SCHUYLER S. KORBAN1,* 1Department of Natural Resources and Environmental Sciences, University of Illinois, 310 Madigan Building, 1201 West Gregory Drive, Urbana, IL 6180; 2Biotechnology Keck... more
... KSENIJA GASIC1, ALVARO HERNANDEZ2 and SCHUYLER S. KORBAN1,* 1Department of Natural Resources and Environmental Sciences, University of Illinois, 310 Madigan Building, 1201 West Gregory Drive, Urbana, IL 6180; 2Biotechnology Keck Center, University of ...
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Research Interests: Genetics, Plant Biology, Biology, Cell Cycle, Abiotic Stress, and 15 moreGene expression, Cell Division, Early development, Gene, Enzyme, Fruit set and development, Microarray Analysis, Heat Shock, Global Gene Expression, cDNA library, Cell Expansion, Differential expression, Fruit Development, Functional Annotation, and Malus domestica
Research Interests: Plant Biology, Biology, Medicine, Sequence Analysis, Expressed Sequence Tags, and 12 moreCluster Analysis, Desiccation, Gene, Malus, Low Temperature, Water Deficit, cDNA library, Biochemistry and cell biology, Gene expression profiling, Physiologia, Horticultural production, and reverse transcriptase polymerase chain reaction
An apple starch-branching enzyme SbeI gene (GenBank Accession No. DQ115404) has been isolated, cloned, and sequenced. The SbeI is a single copy gene in the apple genome, consisting of 14 exons and 13 introns, and covering 6075bp. As... more
An apple starch-branching enzyme SbeI gene (GenBank Accession No. DQ115404) has been isolated, cloned, and sequenced. The SbeI is a single copy gene in the apple genome, consisting of 14 exons and 13 introns, and covering 6075bp. As detected by RT-PCR, the apple SbeI is expressed at very low levels during early stages of fruit development; while, the highest levels of mRNA transcripts are observed at approximately 44 days post-pollination. Besides fruits, the apple SbeI is also expressed in buds and flowers, and very weakly in leaves. The genomic structure of SbeI in apple is strikingly similar to those reported so far in grasses (Poaceae), with exons 4 through 13 being of identical lengths in both apple and grasses. Moreover, structure similarities in exon lengths have also been detected in SbeII genes of both grasses and eudicots. These findings prompted the investigation of the evolutionary process of the Sbe gene family in angiosperms. A total of 26 Sbe sequences, representing an array of monocots and eudicots, are investigated in this study. Phylogenetic analysis has suggested that Sbe genes have duplicated into SbeI and SbeII prior to the divergence of moncots from eudicots. The SbeII gene is further duplicated into SbeIIa and SbeIIb prior to the radiation of grasses; however, it is not yet clear whether this duplication event has occurred before or after the radiation of the eudicots.