Jugpreet Singh

• Ph.D
• Assistant Professor - Tropical Fruit Breeding & Genetics at University of Florida

Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underly...

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 s...

Key message We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soy‑ bean is confrmed against Apios and Vigna species. Abstract Apios (Apios americana; “apios”), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans....

Venturia inaequalis , the causal fungal pathogen of apple scab, has evolved with its Malus hosts during apple domestication. This co‐evolution has resulted in a genetic structure in V . inaequalis populations from Europe and central Asia based on host species and geographic isolation. However, it is not yet clear if geographic isolation has led to...

Pear (Pyrus spp) is one of the most common fruit crops grown in temperate regions worldwide. Genetic enhancement of fruit quality is a fundamental goal of pear breeding programs. The genetic control of pear fruit quality traits is highly quantitative, and development of high-density genetic maps can facilitate fine-mapping of quantitative trait loc...

Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resist...

Genomic, genetic, and archaeobotanical findings have confirmed that alongside interspecific hybridizations between Malus sieversii from Central Asia and wild species along the Silk Road, segmental duplications, point mutations, and clonal propagation have led to the fixation of traits in cultivated apples, unlike in annual crops. Moreover, there is...

Although human-imposed selection is known to have altered plant traits during crop domestication, the effect of selection on host susceptibility or resistance is not well understood. Moreover, the domestication of perennial tree fruit crops, unlike annual crops, was driven by hybridization, clonal propagation, and selection of desirable phenotypes,...

Fire blight, caused by epiphytotic gram‐negative bacteria Erwinia amylovora, is the most destructive bacterial disease of apple (Malus spp.). Genetic mechanisms of fire blight resistance have mainly been studied using traditional biparental quantitative trait loci (QTL) mapping approaches. Here, we use large‐scale historic shoot and blossom fire bl...

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Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for precise control of sugar and oxygen levels. We compared responses to oxygen (21 and 0.2%) in the pres...

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...

Apios americana an herbaceous perennial legume with climbing, vinous habit, produces underground stem tubers along stolons A americana was wild harvested by Native Americans throughout eastern North America There is also some evidence of cultivation and transport of landraces Early historical records of Apios in North America describe its important...

Over the last 40 years, several researchers have worked to develop improved cultivars of Apios americana. Notable improvements have been made in yield and tuber size. Research over this period has also led to better understanding of genetic and genomic limitations (e.g. sterile triploid populations) and characteristics of floral biology (an unusual...

Abstract 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...

Fire blight remains a serious threat to commercial apple production in the USA and worldwide. Other diseases and spray damage can result in fire blight-like symptoms that can lead to misdiagnosis and affect disease management strategies. Accurate and timely detection of the fire blight pathogen, Erwinia amylovora, is extremely important to deploy a...

Erwinia amylovora causes fire blight, the most devastating bacterial disease of apples and pears in the United States and worldwide. The model E. amylovora strain Ea1189 has been extensively used to understand bacterial pathogenesis and molecular mechanisms of bacterial-plant interactions. In this work, we sequenced and assembled the de novo genome...

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...

Apple scab, caused by Venturia inaequalis, 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 resis...

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...

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...

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 t...

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 rang...

Background Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora (Burr.) Winslow et al., of apple scion cultivars, 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 mass prov...

Apple cultivars with durable resistance are needed for sustainable management of fire blight, the most destructive bacterial disease of apples. Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples, more research is needed to understand the molecular mechanisms underlying host-pathogen interac...

An unusual decline and collapse of young established trees known as “rapid apple decline” (RAD) has become a major concern for apple growers, particularly in the northeastern United States. This decline is characterized by stunted growth, pale yellow to reddish leaves, and tree collapse within weeks after onset of symptoms. We studied declining app...

Weather dataset obtained from 2013 to 2017 from Network for Environment and Weather Applications (NEWA). Data represent the mean values of monthly observations obtained from the weather stations located in Phelps, Farmington, and Sodus, New York. (DOCX)

Different bacterial classes detected by 16S sequencing. Analysis was conducted using rhizosphere, soil, root, and shoot samples from asymptomatic and symptomatic ‘HoneyCrips’ trees. (XLSM)

The ‘HoneyCrisp’ orchard block with rapid apple decline (RAD) selected for this study in Wayne County, NY. The arrows identify row numbers in the orchard block (A). Schematic distribution of asymptomatic (green) and RAD symptomatic (yellow) apple ‘HoneyCrisp’ trees in the study orchard (B-C). Samples from three sets of trees (two asymptomatic neigh...

Temperatures over the four winter months (December-March) over five years at three locations near the studied orchards. The average temperature was obtained for all four months. The number of extreme cold days were calculated by counting number of days with temperatures below -10°C. (DOCX)

Different fungus classes detected by ITS sequencing. Analysis was conducted using rhizosphere, soil, root, and shoot samples from asymptomatic and symptomatic ‘HoneyCrisp’ trees. (XLSM)

The five-year average rainfall data for the ‘HoneyCrisp’ orchard block with rapid apple decline (RAD). Twelve month precipitation (mm) data was obtained for Phelps, Farmington, and Sodus, New York from 2013 to 2017. (TIFF)

Pear (Pyrus; 2n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny in a timely and cost‐effective manner. Genotyping arrays can provide fast, efficient, and high‐throug...

Identification of transcripts between markers flanking quantitative trait loci (QTL) for root length under control condition (rlc), and shoot length under control condition (slc), shown in Table 2.

Annotations of transcripts in the QTL regions that have potential connections to stress adaptation.

The genetic map of rice constructed with polymorphic SNP markers showing linkage groups 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12. The chromosomal location is marked on the left and the marker positions on the genome sequence on the right. The graphical representation was done using MapChart software.

Scatter plot showing the relationship between linkage map distances (cM) and physical distances (Mb) among 12 chromosomes indicated by red lines with red squares representing the markers mapped for each of the 12 chromosomes. The recombination rate (cM/Mb) is shown using black lines.

Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to i...

Genes that control “Domestication Syndrome” traits were direct targets of selection, like those controlling increased seed size in the common bean. However, selection for this trait brought about unintentional selection on genes controlling seedling growth. We hypothesized that wild and domesticated plants have different early seedling growth patte...

Background Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well ch...

Current sequencing techniques are capable of generating a good representation of the sequence of an organism’s genome or transcriptome inexpensively. Such sequencing facilitates the genetic characterization of various ” orphan ” plant species, including some that may have a promising future as new crops. We used transcriptome sequencing to identify...

LIS (legumeinfo.org) is a resource for trait genetics and comparative genomics for legumes. The site hosts annotated genomes for nine species: common bean, chickpea, pigeonpea, Medicago truncatula, Lotus japonicus, mungbean, soybean (SoyBase.org) and two Arachis species (PeanutBase.org). A major effort at LIS is to leverage data from information-ri...

Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these...

Quantitative trait loci (QTL) analysis is often the starting point for dissecting underlying genetic mechanisms of complex traits. To make use of the many QTL mapping studies in legumes, methods are needed for integrating QTLs from various studies within a species. We describe the approaches used in public databases for soybean (soybase.org), commo...

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 genomi...

We present here the first comprehensive genetic characterization of wild melon accessions from northern India. The genetic diversity among 43 wild melon accessions collected from the six agro-ecological regions of the Punjab State of India was assessed by measuring variation at 16 Simple Sequence Repeat (SSR) loci, morphological traits of plant hab...

We present here the first comprehensive genetic characterization of snapmelon landraces from the humid tropics of eastern India. The genetic diversity among 42 snapmelon landraces collected from four agro-ecological regions of eastern India (eight agro-ecological subregions) was assessed by measuring variation at 16 simple sequence repeat (SSR) mar...

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...

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. Howev...

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...