Josh Clevenger

Mars-Wrigley Confectionery

Key message We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Abstract Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease...

Late leaf spot (LLS) disease is an omnipresent peanut (Arachis hypogaea L.) foliar disease that causes significant yield loss. Integrating host resistance to reduce yield loss and management costs from this disease is highly desirable. In addition to disease resistance, market demand for high‐oleic peanut is on the rise due to its improved oxidativ...

Seed dormancy is an important breeding trait for the development of certain types of peanut cultivars. Peanut cultivars with seed dormancy can inhibit preharvest sprouting in which the sprouting may increase susceptibility to preharvest aflatoxin contamination. The recombinant inbred line (RIL) mapping population derived from a cross of Tifrunner,...

Blanchability is an often overlooked, but important trait for peanut breeding. The process of blanching, removing the skin, is an important step in the processing of raw nuts for manufacturing. Under strong genetic control and requiring considerable effort to phenotype, blanchability is conducive for marker-assisted selection. We used QTL sequencin...

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhi...

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut...

Cultivated peanut ( Arachis hypogaea ) is one of the most widely grown food legumes in the world, being valued for its high protein and unsaturated oil contents. Drought stress is one of the major constraints that limit peanut production. This study’s objective was to identify the drought-responsive genes preferentially expressed under drought stre...

Next Generation sequencing was a step change for molecular genetics and genomics. Illumina sequencing in particular still provides substantial value to animal and plant genomics. A simple yet powerful technique, referred to as QTL sequencing (QTL-seq) is susceptible to high levels of noise due to ambiguity of alignment of short reads in complex reg...

Symbiotic nitrogen fixation (SNF) inside root-nodules is a primary and sustainable source of soil nitrogen. Understanding nodule development and metabolism in crop legumes may lead to more effective SNF in agriculture. Peanut (Arachis hypogaea) is an economically important allotetraploid legume with non-canonical nodule developmental features. Rece...

Aspergillus flavus and Aspergillus parasiticus produce carcinogenic aflatoxins during crop infection, with extensive variations in production among isolates, ranging from atoxigenic to highly toxigenic. Here, we report draft genome sequences of one A. parasiticus isolate and nine A. flavus isolates from field environments for use in comparative, fu...

Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae . However, less progress has been made for A. flavus . As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL...

Key message: Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection. Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the g...

Cultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of...

An unusual 5-Small Leaflet mutant plant was found within the ‘Georgia Green’ runner-type peanut (Arachis hypogaea L.) cultivar. Subsequent selfing has not established a true-breeding 5-Small Leaflet genotype. It continues to segregate normal and 5-Small Leaflet plants but with a reduced number of normal leaf plants upon selection for 5-Small Leafle...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Developing markers linked to key traits has been a focus of peanut genomics in the post‐genome era. Multiple disease resistance traits have been found to be qualitative and controlled by major quantitative trait loci (QTL) or even single genes while others are more complex. Southern stem rot (stem rot in short) is a devastating disease of peanut ca...

Flowering time is crucial in watermelon (Citrullus lanatus) production as it determines time of fruit set. Early flowering is desirable because it enables crops to escape biotic and abiotic stresses that are intensified by long production cycles. Production of seedless watermelon is also reliant on synchronized flowering of diploid pollenizers and...

Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic...

Egusi watermelon (Citrullus mucosospermus), a close relative of sweet watermelon, is an economically important crop grown in many West African countries for its protein and lipid rich edible seeds. Egusi watermelon seeds have a thick, fleshy mucilaginous seed coat layer surrounding the seed coat which is unique to egusi watermelon. The egusi seed t...

Different species of edible seed watermelons (Citrullus spp.) are cultivated in Asia and Africa for their colorful nutritious seeds. Consumer preference varies for watermelon seed coat color. Therefore, it is an important consideration for watermelon breeders. In 1940s, a genetic model of four genes, R, T, W and D, was proposed to elucidate the inh...

Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources o...

Background Tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) are three serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the genes underlying resistance to those diseases in peanut have not been well studied. We conducted a genome-wide association study (GW...

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions...

Elongated tomato fruit shape is the result of the action of the fruit shape genes possibly in coordination with the phytohormone auxin. To investigate the possible link between auxin and the fruit shape genes, a series of auxin (2,4-D) treatments were performed on the wild-type and the fruit shape near-isogenic lines (NILs) in Solanum pimpinellifol...

Single nucleotide polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and codominant. However, the discovery of true SNPs in polyploid species is difficult. Peanut (Arachis hypogaea L.) is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Axio...

Figure S3 Frequency histogram of the percentage of missing data points in WGRS of 91 RILs with 16 674 polymorphic SNPs in the population.

Figure S4 Distribution of markers on linkage groups.

Figure S6 Genetic and QTL map of major QTLs (>10% PVE) comprising SNP and SSR markers in Tifrunner × GT‐C20 population in peanut (Pandey et al., 2017a).

Figure S2 Percentage reads mapped to the diploid reference A‐ and B‐genome in each RIL and the two parents.

Figure S5 QTL maps showing the major QTL peaks at different LODs on vertical axis.

Table S1 Phenotypic variation of diseases (ELS, LLS and TSWV) in T‐population parents and RILs. Table S2 Overview of the WGRS data and alignment to the reference genome. Table S3 Summary of SNPs detected between Tifrunner and GT‐C20 and SNPs used in RIL population. Table S4 Number of homeologus and translocated markers. Table S5 Effect of major...

Figure S1 Phenotypic distribution of ELS, LLS and TSWV in T‐pop RILs during different seasons.

Fusarium wilt, Fusarium oxysporum f. sp. niveum (FON), of watermelon (Citrullus lanatus) is a fungal pathogen that causes significant yield losses in the US watermelon industry. FON damages watermelon through invasion of the root system and remains a difficult pathogen to manage due to its long-lasting survival spores which persist in the soil. Che...

Background Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled b...

Cultivated peanut (Arachis hypogaea L.) is an important oilseed crop that is grown extensively in Africa, Asia and America. The diseases early and late leaf spot severely constrains peanut production worldwide. Because multiple genes control resistance to leaf spot diseases, conventional breeding is a time-consuming approach for pyramiding resistan...

ANOVA of phenotypic data for LLS in 2015 and 2016 and for ELS in 2016 and 2017.

List of resistance genes identified on B05 for LLS and on A03 and B04 for ELS.

Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs) are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads...

Whole genome re‐sequencing (WGRS) of mapping populations has facilitated development of high‐density genetic linkage maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases...

Single Nucleotide Polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and co-dominant. However, the discovery of true SNPs especially in polyploid species is difficult. Peanut is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Arachis 58k Af...

In peanut (Arachis hypogaea L.), most agronomically important traits such as yield, disease resistance, and pod and kernel characteristics are quantitatively inherited. Phenotypic selection of these traits in peanut breeding programs can be augmented by marker-assisted selection. However, reliable associations between unambiguous genetic markers an...

Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploi...

Improving seed quality traits is one of the most important goals in peanut breeding. Since many of these traits are relatively difficult to phenotype, an alternative indirect selection by markers is needed. Yet, peanut has very low degree of polymorphism especially among cultivated varieties that hindered the development of mapping tools. The aim o...

Resistance to root-knot nematode was introgressed into cultivated peanut Arachis hypogaea from a wild peanut relative, A. cardenasii and previously mapped to chromosome A09. The highly resistant recombinant inbred RIL 46 and moderately resistant RIL 48 were selected from a population with cv. Gregory (susceptible) and Tifguard (resistant) as female...

For crops with a narrow cultivated genetic base, incorporating beneficial alleles from related species through alien introgression widens the genetic base and provides key resistances to disease and abiotic stresses. Fine mapping of these introgressions can increase the efficiency of marker-assisted selection for breeding programs. To facilitate hi...

An image processing software for analyzing seed, leaf, stem, ... coverage infection, this version was designed mainly for analyze peanut seeds which infected by GFP-Aspergillus-flavus strain. The software and full description are available at: https://github.com/w-korani/SICIA.

An extended image processing software of SICIA version I for analyzing seed, leaf, stem, ... coverage infection, SICIA-I was designed mainly for peanut seeds which infected by GFP-Aspergillus-flavus strain. However, this version (SICIA-II) is suitable for a large application, for other species and other methods of infection. The software and full d...

Aflatoxin contamination is a major economic and food safety concern for the peanut industry that largely could be mitigated by genetic resistance. To screen peanut for aflatoxin resistance, ten genotypes were infected with a green fluorescent protein (GFP)—expressing Aspergillus flavus strain. Percentages of fungal infected area and fungal GFP sign...