Vegetable Breeding and Genetics
Plant and Environmental Sciences Department, Coastal Research and Education Center
Office: Coastal Research and Education Center
Ph.D. Plant Biology
The University of Texas at Austin 2013
The University of Texas at Austin 2005
The Southeastern region of the United States represents a critical component of vegetable production for our nation both in terms of diversity of cropping systems (including watermelon, melon, sweet potato, Brassica leafy greens, tomatoes and peppers) and total quantity, with over 300,000 acres of vegetables planted in 2018, worth an estimated $1.8 billion. The warm, wet climate of the Southeastern U.S. presents ideal conditions for many crop pathogens, leading to extreme disease pressure in this region. Host-plant resistance represents the most effective and sustainable form of disease management. As we seek to expand well-established and emerging markets to improve agricultural profits and crop diversity both locally in South Carolina and regionally in the Southeastern U.S ., locally-adapted germplasm (particularly heat tolerance and disease resistance) will have to be identified to ensure a sustainable production system. The focus of my research is genomics-assisted breeding of vegetable crops through 1) development of genomic resources, 2) exploring the genetic and phenotypic diversity of the USDA germplasm repositories, 3) identifying QTL associated with resistance to heat and disease, 4) developing and testing molecular markers associated with phenotypes of interest, and 5) population development for marker validation, trait introgression and gene pyramiding.
Extension and Outreach
Although my appointment is 100% research, communication with stakeholders (growers, processors, extension agents, etc.) is critical to identify both the most urgent issues with vegetable production in South Carolina and the most important trait characteristics for each crop. Breeding progress must be assessed and guided by frequent interaction with growers. Improved vegetable breeding lines and/or cultivars developed in the Branham lab will be grown in on-farm variety trials and Clemson CREC field days where they can evaluated by relevant stakeholders (interested growers and seed companies).
1. Branham SE, Wechter WP, Ling KS, Chanda B, Massey L, Zhao G, Guner N, Bello M, Kabelka E, Fei Z, Levi A. 2020. QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus. Theoretical and Applied Genetics 133(2):677-687.
2. Wu S, Wang X, Reddy U, Sun H, Bao K, Gao L, Mao L, Patel T, Ortiz C, Abburi VL, Nimmakayala P, Branham SE, Wechter P, Massey L, Ling KS, Kousik C, Hammar SA, Tadmor Y, Portnoy V, Gur A, Katzir N, Guner N, Davis A, Hernandez AG, Wright CL, McGregor C, Jarret R, Zhang X, Xu Y, Wehner TC, Grumet R, Levi A, Fei Z. 2019. Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the US National Plant Germplasm System watermelon collection. Plant biotechnology journal 17(12):2246-2258.
3. Branham SE, Levi A, Wechter WP. 2019. QTL mapping identifies novel source of resistance to Fusarium wilt race 1 in Citrullus amarus. Plant Disease 103(5):984-9.
4. Potnis N*, Branham SE*, Jones J, Wechter WP. 2019. Genome-wide Association Study of Resistance to Xanthomonas gardneri in USDA Pepper (Capsicum) Collection. Phytopathology 109(7):1217-1225. (*Co-first authors)
5. Branham SE, Levi A, Katawczik ML, Wechter WP. 2019. QTL mapping of resistance to bacterial fruit blotch in Citrullus amarus. Theoretical and Applied Genetics 132(5):1463-1471.
6. Branham SE, Farnham MW. 2019. Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing. Euphytica 215: 34.
7. Branham SE, Wechter WP, Lambel S, Massey L, Ma M, Fauve J, Farnham MW, Levi A. 2018. QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon. Molecular Breeding 38: 139.
8. Wadl PA, Olukolu BA, Branham SE, Jarret RL, Yencho GC, Jackson DM. 2018. Genetic diversity and population structure of the USDA sweetpotato (Ipomoea batatas) germplasm collections using GBSpoly. Frontiers in Plant Science 9:1166.
9. Branham SE, Levi A, Katawczik M, Fei Z, Wechter WP. 2018. Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f.sp. melonis race I resistance QTL. Theoretical and Applied Genetics 131(4): 829-837.
10. Branham SE, Farnham MW, Robinson SM, Wechter WP. 2018. Identification of resistance to bacterial leaf blight in the USDA collard collection. HortScience 53(6): 838-841.
11. Branham SE, Vexler L, Meir A, Tzuri G, Levi A, Wechter WP, Tadmor Y, Gur A. 2017. Genetic mapping of a major co-dominant QTL associated with beta-carotene accumulation in watermelon. Molecular Breeding 37: 146.
12. Stansell Z, Bjorkman T, Branham SE, Couillard D, Farnham MW. 2017. Use of a quality trait index to increase the reliability of phenotypic evaluations in broccoli. HortScience 52(11): 1490-1495.
13. Branham SE, Farnham MW. 2017. Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines. Euphytica 213:84-89.
14. Branham SE, Stansell ZJ, Couillard DM, Farnham MW 2017. Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing. Theoretical and Applied Genetics 130(3): 529-538.
15. Branham SE, Levi A, Farnham MW, Wechter WP. 2017. A genotype-by-sequencing-single nucleotide polymorphism based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides. Theoretical and Applied Genetics 130: 319-330.
16. Daley J, Branham SE, Levi A, Hassel R, Wechter WP. 2017. Mapping resistance to Alternaria cucumerina in Cucumis melo. Phytopathology 107(4): 427-432.
17. Branham SE, Wright S, Reba A, Morrison GD, Linder CR. 2016. Genome-wide association study in Arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants. Journal of Heredity 107(3): 257-65.
18. Branham SE, Wright SJ, Reba A, Linder CR. 2016. Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition. Journal of Heredity 107(3): 248-256.
19. Pelc SE, Couillard D, Stansell ZJ, Farnham MW. 2015. Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops. The Plant Genome 8(3): 1-11.
20. Pelc SE, Linder CR. 2015. Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana. Ecology and Evolution 5(1): 164-171.
21. Simpson BB, Arroyo MTK, Pelc SE, Dias de Moraes M, McDill J. 2009. Phylogeny and evolution of Perezia (Asteraceae: Mutisieae: Nassauviinae). Journal of Systematics and Evolution 47(5): 431-443.