Progress 02/01/18 to 01/31/21
Outputs
Target Audience:The target audiences include students in the graduate level Plant Breeding course taught by the PI, and attendees who presented and watched the PI's talk in the American Society for Horticultural Science (ASHS) 2020 annual conference and members who find it onthewebsite. A graduate student is supported by this project. Apost-doctoral scientist, who also contributed, was able to obtainfirst-hand experience in genotyping germplasm and phenotyping for heat stress related traits. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided hands on training opportunities to underrepresented populations from HBCUs. Undergraduate students and a graduate student gained first hand experience on maintaining germplasm, conducting heat stress experiments, and collecting data related to photosystem apparatus using fluor pen and other devices. Post-doctoral scientist Dr. Krishnanand Kulkarni also obtained first-hand experience in the collection of data for this project and characterization of germplasm, analysis of Genome Wide Associations for the traits under study. How have the results been disseminated to communities of interest?We disseminated the information by publishing the results in MDPI's International Journal of Molecular Science (IJMS), the PI presented findings in 2020 ASHS (American Society for Horticultural Sciences) conference. The graduate student developed a thesis from part of this project and presented it to the college. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In this project we have utilized 62 accessions derived from an interspecific cross of diploid Vaccinium corymbosum and Vaccinium darrowii and 37 accessions including cultivars for phenotyping heat stress tolerance and its related traits. These 99 accessions were also genotyped by the Illumina sequencing protocol. These accessions include northern highbush (NHB, primarily V. corymbosum), southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). These blueberry samples were genotyped for variant identification. Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp), which were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence. An average of 2.8 million reads with a tag per sample were successfully mapped to the reference genome, which corresponds to an overall mapping rate of 83% to the genome. From the alignments, we identified 2,244,039 SNPs with the 99 selected accessions. After stringent SNP filtering, we obtained 92,048 SNPs distributed across the V. corymbosum reference genome, with an average of five SNPs per 1-kb genome length. The number of filtered SNPs mapped to the 12 scaffolds ranged from 6191 SNPs for VACCDSCAFF12 to 8994 for VACCDSCAFF2. The SNP information was used for principal component analysis, which revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. In this study, the overall fixation index (FST) and the nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, whereas haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. Genetic lineage distribution by admixture analysis of the 60 F2 progeny derived from BNJ16-5 cross was overall 50%, with wide variation for the admixture coefficients (from 0 to 1). Also, the admixture analysis identified progenies with <10% parental lineage from either species, which can be of great importance in breeding blueberries with desirable traits such as heat stress tolerance and fruit composition.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Kulkarni KP, Vorsa N, Natarajan P, Elavarthi S, Iorizzo M, Reddy UK, Melmaiee K. Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives. International Journal of Molecular Sciences 2020 Dec 26;22(1):163.
doi: 10.3390/ijms22010163. PMID: 33375261; PMCID: PMC7796047.
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Progress 02/01/19 to 01/31/20
Outputs
Target Audience:Undergraduate and graduate students in my lab as they are engaged in research and lab meetings. STEM majors from Delaware State University as my students presented the project results at University wide research day and summer research symposium. Interested participants at National Association of Plant Breeders (NAPB) meeting. Additionally, Blueberry growers and enthusiasts from Mid-Atlantic region who participated in our blueberry workshops. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided me opportunities to train four undergraduate students working in my lab and the graduate student who is directly working on this project. This project gave me the opportunity to collaborate established scientists like Dr. Nicholi Vorsa from Rutgers University and develop molecular markers for high temperature stress tolerance in blueberries. How have the results been disseminated to communities of interest?Project results were disseminated to students and researchers attending the DSU research symposium, NAPB meeting and ARD meeting in the form of published abstracts, poster displays and oral presentations. Dr. Melmaiee will utilize some of the data generated from this project to train graduate students in her Advanced molecular breeding class. What do you plan to do during the next reporting period to accomplish the goals?Phenotype F2 population for high temparature stress tolerance for the second year. Characterize SNP markers, develop genome maps and observe genetic relatedness or distance among the wild blueberry germplasm and find associations for high temparature stress tolerance and its related traits.
Impacts
What was accomplished under these goals?
1. Phenotyping of the germplasm which contains genetic backgrounds of V. corymbosum (northern high bush type- high temperature susceptible) and V. darrowii (southern evergreen shrub-high temperature stress tolerant type) 2. Developed first ever reference transcriptome for V. corymbosum and V. darrowii 3. Sequenced both corymbosum and darrowii transcriptome when plants were stressed under 45°C for 0, 6 and 9 hrs. 4. Identified pathways altered during heat stress in blueberries. 5. A portion of F2 plants and 56 accessions from diversity panel were genotyped by sequencing (GBS) and SNPs were identified. 6. 15,414 SSRs (simple sequence repeats) were identified from our transcriptome sequences and PCR primers were developed for all these primers bioinformatically. 7. F2 population was phenotyped for high temparture stress tolerance during 2019 summer.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2019
Citation:
proquest.com
NAPB website for 2019
Youtube.com with keyword serach Jodi Callwood and Blueberry
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Progress 02/01/18 to 01/31/19
Outputs
Target Audience:Graduate student and I presented experimental results at 2019 Delaware State University's research day symposium, 2018 National Association of Plant Breeders meeting and Association of 1890 Research directors meeting Changes/Problems:Our gradaute student started later than expected hence we will be requesing for no cost extension of one year. What opportunities for training and professional development has the project provided?This project provided me opportunities to train three undergraduate students working in my lab and the graduate student who is directly working on this project. This project gave me the opportunity to collaborate established scientists like Dr. Nicholi Vorsa from Rutgers University and develop molecular markers for high temperature stress tolerance in blueberries. How have the results been disseminated to communities of interest?Projects results were dessiminated to students and researchers attending the DSU research symposium, NAPB meeting and ARD meeting in the form of published abstracts, poster displays and oral presentations. Dr. Melmaiee will utilize some of the data generated from this project to traingraduate students in her Advanced molecular breeding class in Fall 2019. What do you plan to do during the next reporting period to accomplish the goals?1. Identify trascriptome derived SSR markers 2. Create DNAlibraries for genotyping by sequencing 3. Identify and characterize SNP markers 4. Develop genome wide selection models
Impacts
What was accomplished under these goals?
1. Phenotyping of the germplasm which contains genetic backgrounds of V. corymbosum (northern high bush type- high temperature susceptible) and V. darrowii (southern evergreen shrub-high temperature stress tolerant type) 2. Developed first ever reference transcriptome for V. corymbosum and V. darrowii 3. Sequenced both corymbosum and darrowiitranscriptome derived when plants were stressed under 45°C for 9 hrs.
Publications
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