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Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM... more
Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p
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Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian... more
Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleoti...
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Background Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this... more
Background Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this study, the hypothesis that rootstocks of higher root vigor provide higher tolerance to fire blight infection in apples is tested. Several apple scion genotypes grafted onto a single rootstock genotype and non-grafted ‘M.7’ rootstocks of varying root vigor are used to assess phenotypic and molecular relationships between root traits of rootstocks and fire blight susceptibility of apple scion cultivars. Results It is observed that different root traits display significant (p
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Apple scab, caused by Venturia inaequalis (Cke.) Wint., is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the... more
Apple scab, caused by Venturia inaequalis (Cke.) Wint., is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, New York, USA, where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. Chlorosis and pinpoint pitting symptoms typical of failed infections by V. inaequalis on hosts bearing the Rvi6 and Rvi7 genes were also observed. We ...
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The fire blight pathogen, Erwinia amylovora(EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains.... more
The fire blight pathogen, Erwinia amylovora(EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains. However, the genomic aspects of population bottlenecks and selection pressure from geographical isolation, host range, and management practices are yet unexplored. We conducted a comprehensive analysis of whole genome sequences of 41 strains to study genetic diversity, population structure, and the nature of selection affecting sub-population differentiation in EA. We detected 72,741 SNPs and 2,500 Indels, representing about six-fold more diversity than previous reports. Moreover, nonsynonymous substitutions were identified across the effector regions, suggesting a role in defining virulence of specific strains. EA plasmids had more diversity than the chromosome sequence. Population structure analysis identified three distinct sub-groups in EA strains, w...
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Maternal control of seed size in the common bean provides an opportunity to study genotype-independent seed weight effects on early seedling growth and development. We set out to test the hypothesis that the early heterotrophic growth of... more
Maternal control of seed size in the common bean provides an opportunity to study genotype-independent seed weight effects on early seedling growth and development. We set out to test the hypothesis that the early heterotrophic growth of bean seedlings is determined by both the relative amount of cotyledon storage reserves and the genotype of the seedling, provided the hybrid genotype could be fully expressed in the seedlings. The hypothesis was tested via comparison of seed weight and seedling growth phenotypes of small-seeded (wild, ~0.10 g) and large-seeded (landrace, ~0.55 g) parents and their reciprocal F1 hybrids. Akaike's Information Criteria were used to estimate growth parameters and identify the phenotypic model that best represented the data. The analysis presented here indicates that the hybrid embryo genotype is not fully expressed during both seed and seedling growth and development. The analysis presented here shows that seed growth and development are controlled ...
The evaluation of plant collections through combination of phenotyping and genomics provides a valuable tool for crop improvement. A study involving multi-year, multi-environment phenotypic evaluation, generation of genomic resources and... more
The evaluation of plant collections through combination of phenotyping and genomics provides a valuable tool for crop improvement. A study involving multi-year, multi-environment phenotypic evaluation, generation of genomic resources and their utilization in mining a collection of Apios americana is presented. Apios is native to central and eastern USA and was once a staple food for Native Americans. It produces protein rich tubers (~16%; 3X to 4X that of Solanum tuberosum) and is cultivated in Japan and South Korea because of its nutritional benefits. The phenotypic evaluation of 53 Apios accessions utilizing 20 traits derived from above and belowground growth parameters was conducted in Iowa, Virginia, and Pennsylvania with lines that produced a range of tuber yields up to 1,515 g per plant. We have generated a reference transcriptome assembly and gene expression atlas, and have genotyped the entire breeding collection using RNA-Seq to produce ~58,000 SNPs scorable across the coll...
PeanutBase (http://peanutbase.org) is a web portal for researchers in peanut genetics, genomics and cultivar development. The genomes of the two wild progenitors of cultivated peanut, A. duranensis and A. ipaensis, have recently been... more
PeanutBase (http://peanutbase.org) is a web portal for researchers in peanut genetics, genomics and cultivar development. The genomes of the two wild progenitors of cultivated peanut, A. duranensis and A. ipaensis, have recently been sequenced and are served from PeanutBase as sequence data for download and as annotated genomes in its browsers along with gene models from related legumes like soybean and common bean. The mapping of molecular markers from various Arachis species, including cultivated peanut, to these genomes has enabled integration of trait information with genomic data. Trait data is being collected and curated from QTL studies and is available at PeanutBase and viewable on interactive maps. We have also compiled Marker Assisted Selection information for some of the important traits and plan to involve experts from the community to continue developing this resource. PeanutBase is concurrently developed with Legume Information System (http://legumeinfo.org) and benefi...
Background Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the... more
Background Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora. Results The genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Compar...
Research Interests: Genetics, Comparative Genomics, Biological Sciences, Software, Plant diseases, and 12 moreQuorum Sensing, Iron, Plasmids, Virulence factor, Plant Pathogen, Erwinia, Host Range, Virulence Factors, Comparative Genomic Hybridization, Molecular Sequence Data, Genomic Islands, and Medical and Health Sciences
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We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species. Apios (Apios americana; "apios"),... more
We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species. Apios (Apios americana; "apios"), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationall...
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Cotyledon reserves are the prime source of nutrition for early heterotrophic seedling growth and development. Larger seeds have more nutrient reserves and support better germination, while smaller seeds are physiologically more active and... more
Cotyledon reserves are the prime source of nutrition for early heterotrophic seedling growth and development. Larger seeds have more nutrient reserves and support better germination, while smaller seeds are physiologically more active and show rapid emergence and growth during early seedling stage. Thus, when investigating genes that control early seedling growth and development, it is important to assess the extent to which genes that control seed size also control, indirectly, heterotrophic seedlings growth. If the latter set of genes exerts a significant control on early growth, then seed size should be considered as a covariate in the genetic analysis of early growth. Seed size effects on early seedling growth should be investigated within the same genotype. One possibility is to control seed size by effecting growth conditions, or by removing one cotyledon. However, parental environmental effects and wounding can bias the results. Instead, we generated F1 seeds from reciprocal ...
Seed size was the principle target of selection during domestication of common bean. An 8 to 10-fold increase in seed size can be observed between landraces and wild accession of the Andean gene pool. This observation raises the question... more
Seed size was the principle target of selection during domestication of common bean. An 8 to 10-fold increase in seed size can be observed between landraces and wild accession of the Andean gene pool. This observation raises the question of whether the increase was nutritionally neutral, or it was accompanied by the preferential accumulation of one of the main seed storage components (protein vs starch). This question was addressed via QTL analysis of seed size, starch and protein content in a RI family (n = 168) generated from a cross between a landrace (G19833) and a wild accession (G23419), both from the Andean gene pool. Seed weight (SW), starch and protein content were obtained from individual seeds of the RI family using near-infrared reflectance (NIR). Seed size was significantly and positively correlated with starch content, and negatively correlated with protein content. As expected, protein and starch contents were negatively correlated. The genotyping-by-sequencing method...
Selection for the most desirable alleles and consequent changes in allele frequencies has accompanied the phenotypic alterations between wild and domesticated populations of various crop plants. These alterations include significant... more
Selection for the most desirable alleles and consequent changes in allele frequencies has accompanied the phenotypic alterations between wild and domesticated populations of various crop plants. These alterations include significant structural and physiological changes. Genetic analysis of various domestication-associated traits has detected genomic regions subjected to selection, and has also led to the identification of major genes that regulate those traits. However, previous analyses of domestication have mainly considered the above-ground plant organs, while root traits have been largely neglected because of underground nature of this organ. This problem was further complicated by time consuming and inaccurate methods of phenotyping root traits by digging and washing roots from the soil. However, it is very likely that changes in root growth and architecture might have happened because selection for particular shoot traits can lead to inadvertent selection for root traits as th...
Continuous selection for the most desirable phenotypes from wild populations during domestication changes allele frequencies at specific targeted loci. Genomic regions subjected to selection have been identified in various domestication... more
Continuous selection for the most desirable phenotypes from wild populations during domestication changes allele frequencies at specific targeted loci. Genomic regions subjected to selection have been identified in various domestication studies, which have further led to the discovery of major genes that control domestication syndrome traits. However, previous analyses of domestication have mainly focused on the above-ground plant organs, while root traits have escaped direct scrutiny due to their underground nature. We hypothesized that domestication-associated changes in root traits are due to selection for above ground traits that also affect roots, and indirect selection for root traits that improve above ground plant performance. To test this hypothesis, we have performed QTL analyses using a RI population of the common bean (Phaseolus vulgaris) derived from the cross [G19833 (landrace) X G23419 (wild accession)]; parents are of Andean origin. A SNP-based linkage map was constr...
... The first comprehensive analysis of genetic variation in this taxon was performed recently (Dhillon et al., 2007), using snapmelon accessions collected from the north-western plains of India. ... The assessment for resistance to CMV... more
... The first comprehensive analysis of genetic variation in this taxon was performed recently (Dhillon et al., 2007), using snapmelon accessions collected from the north-western plains of India. ... The assessment for resistance to CMV was carried out as described in Dhillon et al. ...