Sandra Branham

Assistant Professor of Vegetable Breeding and Genetics
Plant and Environmental Sciences Department, Coastal Research and Education Center

Office: Coastal Research and Education Center
Phone: 843-402-5311

Email: sebranh@clemson.edu

Educational Background

Ph.D. Plant Biology
The University of Texas at Austin 2013

B.A. Biology
The University of Texas at Austin 2005

Research Interests

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, disease introgression and gene pyramiding.

On-going projects in my lab address issues in several crop systems including Brassicas, spinach, Cucurbits and snapbeans:

• QTL mapping, marker development and breeding for resistance to bacterial leaf blight caused by multiple Pseudomonas species in Brassica leafy greens and spinach. Bacterial leaf blight has been devastating leafy greens production in the state and there are no effective chemical control options available. The availability of resistant varieties would increase profits and decrease risks for growers.

• Improvement of collard green germplasm for commercial production in South Carolina. The USDA PI collection of collard greens and commercial cultivars were evaluated in variety trials in fall fields in Charleston. Accessions have been selected for initiate a breeding program to fulfill demands of the processing and fresh market industries in South Carolina. The breeding objectives are to improve yield, erect habit, early vigor, color and delayed bolting. Development and release of a disease resistant OP variety that has an erect habit would make collard production more sustainable. There are currently only a few commercial cultivars available and hybrid seed is too expensive for growers to make a profit to grow for the processing market.

• Evaluation of spinach germplasm for fall production in South Carolina. The USDA PI collection of spinach and commercial cultivars are being evaluated in variety trials in fall fields in Charleston. Recurrent mass selection of the highest yielding accessions is being used to initiate a spinach breeding program to release processing spinach cultivars adapted to South Carolina growing conditions.

• Marker-assisted breeding of Fusarium wilt resistance from citron melon into cultivated watermelon.
Fusarium wilt resistance markers will be validated in an interspecific citron melon/watermelon population, and then we will proceed with marker-assisted backcross breeding. There are currently no edible cultivars available with resistance to race 2 of Fusarium wilt. Development of a diploid watermelon breeding line with this resistance in an elite background would allow industry breeders to develop resistant triploid watermelon.

• Marker-assisted backcrossing of multi-disease resistance into melon. KASP markers tightly linked to resistance to Fusarium oxysporum f. sp. melonis races 1 and 2, powdery mildew race 1
and sulfur phytotoxicity were developed in melon. They will be used for marker-assisted backcrossing into melon cultivars with superior flavor. Development of a multiple-disease resistant melon cultivar would have the potential to increase profits for growers, especially for the specialty crop market.

• Genetic diversity and population structure of the USDA SnAP bean association mapping panel. Genotyping-by sequencing will be used to examine the genetic diversity, population structure and phylogenetic relationships of the accessions within the USDA SnAP bean association panel. Linkage disequilibrium decay will be estimated to determine the potential resolution for genome-wide association studies and the number of markers necessary to capture all haplotype blocks. The diversity panel can then be used to map QTL for a wide range of phenotypes and would be a valuable resource for snap bean breeding.

• Genome-wide association study of heat tolerance in snap beans. The SnAP diversity panel will be evaluated for heat tolerance in two field trials and a greenhouse trial. A genome-wide association study will be used to identify heat tolerance QTLs for future breeding efforts. Development and release of a snap bean variety could extend the growing season for snap beans in South Carolina and protect growers from losses due to unexpected heat waves.

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 be evaluated by relevant stakeholders (interested growers and seed companies).

Publications

1) *Ganaparthi V, Rennberger G, Wechter WP, Levi A, Branham SE. 2023. Genome-wide association mapping and genomic prediction of Fusarium wilt race 2 resistance in the USDA Citrullus amarus collection. Plant Disease. Accepted.
2) Wu S, Sun H, Gao L, Branham SE, McGregor C, Wu Y, Kousik C, Wechter WP, Levi A, Fei Z. 2023. A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnology Journal. Accepted.
3) Rennberger G, Branham SE, Wechter WP. 2023. Genome-wide Association Study of Resistance to Pseudomonas syringae in the USDA Collection of Citrullus amarus. Plant Disease. https://doi.org/10.1094/PDIS-04-23-0795-RE.
4) Toporek SM, Branham SE, Keinath AP, Wechter WP. 2023. QTL Mapping of Resistance to Pseudoperonospora cubensis Clade 2, Mating Type A1, in Cucumis melo and Dual-Clade Marker Development. Theoretical and Applied Genetics 136(4): 91.
5) Wechter WP, Wang H, Branham SE. 2023. First Report of Bacterial Leaf Spot on Spinach (Spinacia oleracea) Caused by Pseudomonas sp. in South Carolina. Plant Disease 107(3): 935.
6) Waldo BD, Branham SE, Levi A, Wechter WP, Rutter WB. 2022. Distinct genomic loci underlie quantitative resistance to Meloidogyne enterolobii galling and reproduction in Citrullus amarus. Plant Disease. https://doi.org/10.1094/PDIS-09-22-2228-RE.
7) Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Branham SE, Kousik S, Wechter WP, Levi A, Grumet R, Zheng Y, Fei Z. 2022. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Research 51(D1): D1457-D1464.
8) Vaughn JN, Branham SE, Abernathy BL, Hulse-Kemp AM, Rivers A, Levi A, Wechter WP. 2022. Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon. Nature Communications 13(1): 7897.
9) Katuuramu D, Branham SE, Levi A, Wechter WP. 2022. Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon. Plant Disease 106(7): 1952-1958.
10) Caputo G, Branham SE, Cutulle M. 2021. Evaluation of Chemical Seed Treatment to Reduce Injury Caused by Preemergent Herbicides on Direct-seeded Turnips and Collard Greens. HortScience 56(12): 1516-1520.
11) Kousik CS, Ikerd JL, Wechter WP, Branham SE, Turechek W. 2021. Broad resistance to fruit rot in USVL watermelon germplasm lines to isolates of Phytophthora capsici from across USA. Plant Disease 106(2): 711-719.
12) Branham SE, Kousik CS, Mandal M, Wechter WP. 2021. QTL mapping of resistance to powdery mildew race 1 in a recombinant inbred line population of melon. Plant Disease 105(12): 3809-3815.
13) Toporek S, Branham SE, Katawczik M, Keinath AP, Wechter WP. 2020. QTL Mapping of Resistance to Pseudoperonospora cubensis Clade 1, Mating Type A2, in Cucumis melo. Theoretical and Applied Genetics 134(8): 2577-2586.
14) Branham SE, Daley J, Levi A, Hassell R, Wechter WP. 2020. QTL Mapping and Marker Development for Tolerance to Sulfur Phytotoxicity in Melon (Cucumis melo). Frontiers in Plant Science 11:1097.
15) 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.
16) 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.
17) 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.
18) 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)
19) 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.
20) Branham SE, Farnham MW. 2019. Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing. Euphytica 215: 34.
21) 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.
22) 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.
23) 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 1 resistance QTL. Theoretical and Applied Genetics 131(4): 829-837.
24) 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.
25) 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.
26) 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.
27) Branham SE, Farnham MW. 2017. Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines. Euphytica 213:84-89.
28) 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.
29) 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.
30) Daley J, Branham SE, Levi A, HasselRol R, Wechter WP. 2017. Mapping resistance to Alternaria cucumerina in Cucumis melo. Phytopathology 107(4): 427-432.
31) 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.
32) 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.
33) 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.
34) 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.
35) 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.