Genetic Mapping of Greenbug Resistance Loci in Sorghum [ Sorghum Bicolor (L.) Moench] & Expression Analysis of Candidate Genes in Response to Greenbug Infestation

Greenbug is a damaging pest of sorghum in the Great Plains of the United States. This study was taken with the objective to identify the genomic regions contributing resistance to greenbug biotype I using sorghum accession, PI 607900 as the resistance source. To accomplish this objective I undertook two projects involving three independent studies. These three studies involved linkage-based mapping and gene expression studies. The first study was conducted in an F 2 mapping population consisting of 371 individuals developed from a cross of BTx623 (susceptible to greenbug) by PI 607900 (resistant to greenbug) to identify QTLs contributing greenbug resistance in sorghum. The second study was performed to identify and confirm QTLs for greenbug resistance in an intercross population developed from a previously used F 2 mapping population. The third study was carried out to examine the differential expression of candidate genes induced by greenbug using real-time PCR experiments in two contrasting parental lines. I found that two major loci for greenbug resistance were on sorghum chromosome 9 from two independent QTL mapping studies. The second QTL mapping project with an intercross population revealed potential candidate genes in a narrowed confidence interval compared to first project's QTL analysis with the F 2 population. These loci were mapped to a region on chromosome 9 flanked by markers Starssbnm 93-Starssbnm 102. The QTL mapping studies identified two novel loci for greenbug resistance using 48 newly developed nuclear and genic SSRs. The identified greenbug resistance loci were linked to a receptor-like kinase Xa21 -binding protein 3, a gene known to increase Xa21 -mediated resistance in rice. Relative quantification of gene expression in the two parental lines indicated that receptor-like kinase Xa21 -binding protein 3 and map kinase phosphatase were differentially expressed upon greenbug infestation. The markers/QTLs identified in the study will have applications in MAS and mapbased cloning experiments for the improvement of greenbug resistance in sorghum.Department of Plant and Soil Science

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Two decades of association mapping: Insights on disease resistance in major crops

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties

Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers

Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines ‘Tift 99D2B1’ and ‘Tift 454’. DNA from 186 RILs, the parents, and the F1 was used for 96-plex ApeKI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to Pyricularia leaf spot [Pyricularia grisea (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community

<i>Bemisia tabaci</i> on Vegetables in the Southern United States: Incidence, Impact, and Management

Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) is among the most economically important insect pests of various vegetable crops in the Southern United States. This insect is considered a complex of at least 40 morphologically indistinguishable cryptic species. Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) was initially introduced in the United States around 1985 and has since rapidly spread across the Southern United States to Texas, Arizona, and California, where extreme field outbreaks have occurred on vegetable and other crops. This pest creates extensive plant damage through direct feeding on vegetables, secreting honeydew, causing plant physiological disorders, and vectoring plant viruses. The direct and indirect plant damage in vegetable crops has resulted in enormous economic losses in the Southern United States, especially in Florida, Georgia, and Texas. Effective management of B. tabaci on vegetables relies mainly on the utilization of chemical insecticides, particularly neonicotinoids. However, B. tabaci has developed considerable resistance to most insecticides. Therefore, alternative integrated pest management (IPM) strategies are required, such as cultural control by manipulation of production practices, resistant vegetable varieties, and biological control using a suite of natural enemies for the management of the pest

Impact of Planting Date and Insecticide Application Methods on Melanaphis sorghi (Hemiptera: Aphididae) Infestation and Forage Type Sorghum Yield

Studies on the management of the invasive Melanaphis sorghi are essential to refining integrated pest management strategies against M. sorghi in forage sorghum in the USA. The objective of this study was to determine the impact of planting date (early planting and late planting) and in-furrow and foliar insecticide application of flupyradifurone, on M. sorghi infestation and forage sorghum yield in Tifton, Georgia and Florence, South Carolina, USA, in 2020 and 2021. Early planted sorghum supported slightly higher aphid density and severity of infestation as evident in the greater cumulative insect days values in the early planted sorghum at both Florence and Tifton in 2020 and 2021. A single foliar application reduced aphid infestations below the threshold level of 50 aphids per leaf. In contrast, in-furrow insecticidal application in selected plots at both locations significantly suppressed M. sorghi density to near-zero levels. Yield results in Florence in 2020 showed that sorghum yield was over 50% greater in early planted plots compared to late planted plots. Both insecticide treatments (foliar and in-furrow) resulted in significantly higher yield than untreated plots. These data indicate that early planting coupled with in-furrow and foliar insecticide applications can suppress M. sorghi infestations and improve silage production in forage sorghum in the USA