Hamid Ashrafi | North Carolina State University (original) (raw)

Papers by Hamid Ashrafi

Research paper thumbnail of There and back again; historical perspective and future directions for Vaccinium breeding and research studies

Horticulture Research

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically impor... more The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the developme...

Research paper thumbnail of Supplemental Material for Zurn et al., 2020

Four Supplementary Tables for Manuscript G3/2020/401449R1

Research paper thumbnail of Supplemental Material for Yow et al., 2020

Mummy berry disease, caused by the fungal pathogen <i>Monilinia vaccinii-corymbosi</i&gt... more Mummy berry disease, caused by the fungal pathogen <i>Monilinia vaccinii-corymbosi</i> (<i>Mvc</i>), is one of the most economically important diseases of blueberries in North America. <i>Mvc</i> is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of <i>Mvc</i> and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for <i>Mvc</i>. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. Macrosynteny analysis revealed syntenic regions between the <i>Mvc </i>genome and genomes of taxonomically related fungi. A total of 9,405 gene model...

Research paper thumbnail of Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids

Scientia Horticulturae, 2022

Research paper thumbnail of Development of a 63K SNP Array for Gossypium and High-density Mapping of Intra- and Inter-specific Populations of Cotton (G. hirsutum L.)

Research paper thumbnail of Using Spinach to Compare Technologies for Whole Genome Assemblies

Research paper thumbnail of and Inter-specific Populations of Gossypium spp. 2

Research paper thumbnail of Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars

Agronomy, 2021

Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of ... more Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of native species into cultivated germplasm has adapted Vaccinium germplasm to a range of climates and growing conditions for cultivated blueberry. Genetic differences signify phenotypic variance that is observed among blueberry accessions. In addition, variability in geographic and climatic growing conditions between environments or within the same environment across different years may further affect fruit and plant phenotypic expression. As a result, a phenotype is a function of genetic background (G), environment (E), and their interaction (G × E). In addition, other temporally regulated factors such as year (Y) and harvest time (H) impact plant and fruit quality phenotypic variation. Our research aimed to assess the genotypic performance of five blueberry cultivars, including ‘Echota’, ‘O’Neal’, ‘Reveille’, ‘Summit’, and ‘Sunrise’. The selected cultivars were phenotyped for various fru...

Research paper thumbnail of Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

BMC Genomics, 2021

Background Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae ... more Background Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae. Results During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented i...

Research paper thumbnail of Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type

G3 Genes|Genomes|Genetics, 2021

Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of ... more Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was cha...

Research paper thumbnail of A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding

G3&#58; Genes|Genomes|Genetics, 2020

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar ... more A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTLs) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the 'Hillquist' blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble so...

Research paper thumbnail of Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars

Canadian Journal of Plant Science, 2019

Unrooted cuttings of ‘Prestige Red’ and ‘White Star’ poinsettias (Euphorbia pulcherrima Willd.) w... more Unrooted cuttings of ‘Prestige Red’ and ‘White Star’ poinsettias (Euphorbia pulcherrima Willd.) were stored in a box at 10 °C for 0, 2, 4, 6 or 8 days to simulate shipping and holding. Visual root ratings decreased following ≥4 days of storage but did not differ from the non-stored cuttings. Root rating of ‘White Star’ was 0.5 higher and cuttings maintained higher fructose and glucose concentrations compared to ‘Prestige Red’. Glucose (r2 = 0.4824) followed by fructose plus glucose (r2 = 0.4222) were the best predictors of rooting. Carbohydrate maintenance may be an indicator of storage tolerant and better-rooting cultivars.

Research paper thumbnail of 3D point cloud data to quantitatively characterize size and shape of shrub crops

Horticulture Research, 2019

Research paper thumbnail of (13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato

HortScience, 2005

Most cultivars of tomato (Lycopersiconesculentum) are susceptible to early blight (EB), a devasta... more Most cultivars of tomato (Lycopersiconesculentum) are susceptible to early blight (EB), a devastating fungal (Alternariasolani) disease of tomato in the northeast and eastern part of the U.S. The most economic and durable measure of disease control is by using genetic resistance. There is limited EB resistance within the cultivated tomato. However, genetic sources of resistance exist within the tomato-related wild species L. hirsutum and L. pimpinellifolium. Early blight resistance does not follow the gene-for-gene model of host–pathogen interaction. Mapping QTLs conferring horizontal resistance is an effective approach for studying complex resistance traits such as EB. We have developed F2, F3, F4, and an F2:7 derived RIL population of a L. esculentum× L. pimpinellifolium cross and evaluated them for EB resistance under field conditions. Genetic maps were constructed based on the F2 (including 256 RFLP, EST and RGA markers) as well as the RIL population (including over 220 RFLP and...

Research paper thumbnail of Genetics and Breeding of Early Blight Resistance in Tomato

HortScience, 2005

Early blight (EB), caused by the fungus Alternaria solani, is a destructive disease of tomato (Ly... more Early blight (EB), caused by the fungus Alternaria solani, is a destructive disease of tomato (Lycopersicon esculentum) worldwide. Sources of genetic resistance have been identified within related wild species, including green-fruited L. hirsutum and red-fruited L. pimpinellifolium. We have employed traditional protocols of plant breeding and contemporary molecular markers technology to discern the genetic basis of EB resistance and develop tomatoes with improved resistance. Backcross breeding has resulted in the development of germplasm with improved resistance; however, linkage drag has been a major obstacle when using L. hirsutum as a donor parent. To identify and map QTLs for EB resistance, we used several filial and backcross populations derived from interspecific crosses between L. esculentum and either L. hirsutum or L. pimpinellifolium. In each population, an average of seven resistance QTLs were detected. While similar QTLs were detected in different generations of the same...

Research paper thumbnail of Breeding Trait Priorities of the Blueberry Industry in the United States and Canada

HortScience, 2018

Developing new blueberry cultivars requires plant breeders to be aware of current and emerging ne... more Developing new blueberry cultivars requires plant breeders to be aware of current and emerging needs throughout the supply chain, from producer to consumer. Because breeding perennial crop plants (such as blueberry) is time- and resource-intensive, understanding and targeting priority traits is critical to enhancing the efficiency of breeding programs. This study assesses blueberry industry breeding priorities for fruit and plant quality traits based on a survey conducted at commodity group meetings across nine U.S. states and in British Columbia (Canada) between Nov. 2016 and Mar. 2017. In general, industry responses signaled that the most important trait cluster was fruit quality including the firmness, flavor, and shelf life. Fruit quality traits affect price premiums received by producers; influence consumer’s preferences; and have the potential to increase the feasibility of mechanical harvesting, all critical to the economic viability of the industry. There were differences ac...

Research paper thumbnail of {"__content__"=>"Regions Underlying Population Structure and the Genomics of Organ Size Determination in .", "i"=>{"__content__"=>"Capsicum annuum"}}

The plant genome, Nov 1, 2017

Fruits, as an important part of the human diet, have been under strong selection during domestica... more Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers ( L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large-fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis gene...

Research paper thumbnail of A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

Horticulture research, 2016

The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cult... more The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybri...

Research paper thumbnail of Recent advance in carrot genomics

Acta Horticulturae, 2017

In recent years there has been an effort towards the development of genomic resources in carrot. ... more In recent years there has been an effort towards the development of genomic resources in carrot. The number of available sequences for carrot in public databases has increased recently. This has allowed the design of SSRs markers, COS markers and a high-throughput SNP assays for genotyping. Additional molecular tools include the first high-throughput DArT array and the full sequence of organelle genomes. These molecular resources have been successfully used to gain new insights into carrot genetic diversity, organelle genome evolution and to establish the first dense sequence-based linkage maps. Supported by a consortium of private companies, sequencing of the carrot genome is currently ongoing. Its release, will establish a solid framework for carrot genomic studies, opening a new challenging and exciting era for the carrot scientific community.

Research paper thumbnail of New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

Frontiers in Plant Science, 2016

Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanac... more Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.

Research paper thumbnail of There and back again; historical perspective and future directions for Vaccinium breeding and research studies

Horticulture Research

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically impor... more The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the developme...

Research paper thumbnail of Supplemental Material for Zurn et al., 2020

Four Supplementary Tables for Manuscript G3/2020/401449R1

Research paper thumbnail of Supplemental Material for Yow et al., 2020

Mummy berry disease, caused by the fungal pathogen <i>Monilinia vaccinii-corymbosi</i&gt... more Mummy berry disease, caused by the fungal pathogen <i>Monilinia vaccinii-corymbosi</i> (<i>Mvc</i>), is one of the most economically important diseases of blueberries in North America. <i>Mvc</i> is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of <i>Mvc</i> and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for <i>Mvc</i>. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. Macrosynteny analysis revealed syntenic regions between the <i>Mvc </i>genome and genomes of taxonomically related fungi. A total of 9,405 gene model...

Research paper thumbnail of Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids

Scientia Horticulturae, 2022

Research paper thumbnail of Development of a 63K SNP Array for Gossypium and High-density Mapping of Intra- and Inter-specific Populations of Cotton (G. hirsutum L.)

Research paper thumbnail of Using Spinach to Compare Technologies for Whole Genome Assemblies

Research paper thumbnail of and Inter-specific Populations of Gossypium spp. 2

Research paper thumbnail of Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars

Agronomy, 2021

Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of ... more Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of native species into cultivated germplasm has adapted Vaccinium germplasm to a range of climates and growing conditions for cultivated blueberry. Genetic differences signify phenotypic variance that is observed among blueberry accessions. In addition, variability in geographic and climatic growing conditions between environments or within the same environment across different years may further affect fruit and plant phenotypic expression. As a result, a phenotype is a function of genetic background (G), environment (E), and their interaction (G × E). In addition, other temporally regulated factors such as year (Y) and harvest time (H) impact plant and fruit quality phenotypic variation. Our research aimed to assess the genotypic performance of five blueberry cultivars, including ‘Echota’, ‘O’Neal’, ‘Reveille’, ‘Summit’, and ‘Sunrise’. The selected cultivars were phenotyped for various fru...

Research paper thumbnail of Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

BMC Genomics, 2021

Background Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae ... more Background Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae. Results During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented i...

Research paper thumbnail of Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type

G3 Genes|Genomes|Genetics, 2021

Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of ... more Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was cha...

Research paper thumbnail of A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding

G3&#58; Genes|Genomes|Genetics, 2020

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar ... more A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTLs) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the 'Hillquist' blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble so...

Research paper thumbnail of Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars

Canadian Journal of Plant Science, 2019

Unrooted cuttings of ‘Prestige Red’ and ‘White Star’ poinsettias (Euphorbia pulcherrima Willd.) w... more Unrooted cuttings of ‘Prestige Red’ and ‘White Star’ poinsettias (Euphorbia pulcherrima Willd.) were stored in a box at 10 °C for 0, 2, 4, 6 or 8 days to simulate shipping and holding. Visual root ratings decreased following ≥4 days of storage but did not differ from the non-stored cuttings. Root rating of ‘White Star’ was 0.5 higher and cuttings maintained higher fructose and glucose concentrations compared to ‘Prestige Red’. Glucose (r2 = 0.4824) followed by fructose plus glucose (r2 = 0.4222) were the best predictors of rooting. Carbohydrate maintenance may be an indicator of storage tolerant and better-rooting cultivars.

Research paper thumbnail of 3D point cloud data to quantitatively characterize size and shape of shrub crops

Horticulture Research, 2019

Research paper thumbnail of (13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato

HortScience, 2005

Most cultivars of tomato (Lycopersiconesculentum) are susceptible to early blight (EB), a devasta... more Most cultivars of tomato (Lycopersiconesculentum) are susceptible to early blight (EB), a devastating fungal (Alternariasolani) disease of tomato in the northeast and eastern part of the U.S. The most economic and durable measure of disease control is by using genetic resistance. There is limited EB resistance within the cultivated tomato. However, genetic sources of resistance exist within the tomato-related wild species L. hirsutum and L. pimpinellifolium. Early blight resistance does not follow the gene-for-gene model of host–pathogen interaction. Mapping QTLs conferring horizontal resistance is an effective approach for studying complex resistance traits such as EB. We have developed F2, F3, F4, and an F2:7 derived RIL population of a L. esculentum× L. pimpinellifolium cross and evaluated them for EB resistance under field conditions. Genetic maps were constructed based on the F2 (including 256 RFLP, EST and RGA markers) as well as the RIL population (including over 220 RFLP and...

Research paper thumbnail of Genetics and Breeding of Early Blight Resistance in Tomato

HortScience, 2005

Early blight (EB), caused by the fungus Alternaria solani, is a destructive disease of tomato (Ly... more Early blight (EB), caused by the fungus Alternaria solani, is a destructive disease of tomato (Lycopersicon esculentum) worldwide. Sources of genetic resistance have been identified within related wild species, including green-fruited L. hirsutum and red-fruited L. pimpinellifolium. We have employed traditional protocols of plant breeding and contemporary molecular markers technology to discern the genetic basis of EB resistance and develop tomatoes with improved resistance. Backcross breeding has resulted in the development of germplasm with improved resistance; however, linkage drag has been a major obstacle when using L. hirsutum as a donor parent. To identify and map QTLs for EB resistance, we used several filial and backcross populations derived from interspecific crosses between L. esculentum and either L. hirsutum or L. pimpinellifolium. In each population, an average of seven resistance QTLs were detected. While similar QTLs were detected in different generations of the same...

Research paper thumbnail of Breeding Trait Priorities of the Blueberry Industry in the United States and Canada

HortScience, 2018

Developing new blueberry cultivars requires plant breeders to be aware of current and emerging ne... more Developing new blueberry cultivars requires plant breeders to be aware of current and emerging needs throughout the supply chain, from producer to consumer. Because breeding perennial crop plants (such as blueberry) is time- and resource-intensive, understanding and targeting priority traits is critical to enhancing the efficiency of breeding programs. This study assesses blueberry industry breeding priorities for fruit and plant quality traits based on a survey conducted at commodity group meetings across nine U.S. states and in British Columbia (Canada) between Nov. 2016 and Mar. 2017. In general, industry responses signaled that the most important trait cluster was fruit quality including the firmness, flavor, and shelf life. Fruit quality traits affect price premiums received by producers; influence consumer’s preferences; and have the potential to increase the feasibility of mechanical harvesting, all critical to the economic viability of the industry. There were differences ac...

Research paper thumbnail of {"__content__"=>"Regions Underlying Population Structure and the Genomics of Organ Size Determination in .", "i"=>{"__content__"=>"Capsicum annuum"}}

The plant genome, Nov 1, 2017

Fruits, as an important part of the human diet, have been under strong selection during domestica... more Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers ( L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large-fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis gene...

Research paper thumbnail of A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding

Horticulture research, 2016

The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cult... more The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybri...

Research paper thumbnail of Recent advance in carrot genomics

Acta Horticulturae, 2017

In recent years there has been an effort towards the development of genomic resources in carrot. ... more In recent years there has been an effort towards the development of genomic resources in carrot. The number of available sequences for carrot in public databases has increased recently. This has allowed the design of SSRs markers, COS markers and a high-throughput SNP assays for genotyping. Additional molecular tools include the first high-throughput DArT array and the full sequence of organelle genomes. These molecular resources have been successfully used to gain new insights into carrot genetic diversity, organelle genome evolution and to establish the first dense sequence-based linkage maps. Supported by a consortium of private companies, sequencing of the carrot genome is currently ongoing. Its release, will establish a solid framework for carrot genomic studies, opening a new challenging and exciting era for the carrot scientific community.

Research paper thumbnail of New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

Frontiers in Plant Science, 2016

Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanac... more Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.