Genetic Diversity of White Cabbage (Brassica oleracea var. capitata subvar. alba) Inbreed Lines Using SRAP Markers

Year 2024, , 429 - 436, 15.09.2024

Ercan Ekbiç , Cemregül Tırınk

https://doi.org/10.47115/bsagriculture.1509098

Abstract

Genetic diversity assessment is crucial for effective breeding programs and the conservation of plant genetic resources. This study aimed to characterize the genetic diversity of 24 cabbage (Brassica oleracea var. capitata subvar. alba) inbred lines using Sequence-Related Amplified Polymorphism (SRAP) markers. A total of 45 SRAP primer combinations were employed, resulting in the amplification of 258 bands, of which 194 (75.2%) were polymorphic. The polymorphism information content (PIC) values ranged from 0.03 to 0.42, with a mean value of 0.20, indicating relatively low genetic diversity among the studied inbred lines. The major allele frequency (MAF) values varied between 0.54 and 0.99, with an average of 0.83, further confirming the limited genetic diversity. The effective allele number (NE), gene diversity (H), and Shannon information index (I) averaged 1.40, 0.23, and 0.35, respectively. Principal component analysis (PCA) revealed that the first seven principal component axes accounted for 90.59% of the total variance among the cabbage lines, demonstrating that the genetic diversity could be largely explained along a few dimensions. STRUCTURE analysis identified three major genetic clusters, with Cluster 3 exhibiting the highest proportion of genetic composition (40.3%) and the highest level of genetic differentiation (mean Fst = 0.4080). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering analysis, based on the Dice similarity method, produced a dendrogram depicting the genetic relationships among the inbred lines. The Mantel test value r for the UPGMA clustering was 0.78, indicating a good fit between the dendrogram and the original similarity matrix. The study highlights the utility of SRAP markers in assessing genetic diversity and relationships among cabbage inbred lines, providing valuable information for breeding programs and genetic resource management. The identification of genetically distinct clusters and the quantification of genetic variation within and among these clusters can guide future breeding efforts and facilitate the development of improved cabbage varieties with desirable traits.

Keywords

Brassica oleracea, Genetic diversity, Inbred lines, SRAP markers, STRUCTURE analysis, UPGMA clustering

References

• Ahmad R, Farhatullah, Quiros CF, Rahman H, Swati ZA. 2014. Genetic diversity analyses of Brassica napus accessions using SRAP molecular markers. Plant Genet Resour, 12(1): 14-21. https://doi.org/10.1017/S147926211300021X.
• Anonymous. 2021. https://www.drdatastats.com/illere-gore-turkiyede-sebze-uretimi (access date: 05.05.2022).
• Collard BCY, Mackill DJ. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci, 363(1491): 557-572.
• Fahey JW, Zalcmann AT, Talalay P. 2001. The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochemistry, 56(1): 5-51.
• Ferriol M, Pico B, Nuez F. 2003. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet, 107(2): 271-282.
• Framarzpour A, Abdoli-Nasab M, Rezvan Nezhad E, Baghizadeh A. 2021. Evaluation of genetic diversity of rapeseed (Brassica napus L.) cultivars using SRAP markers. J Agric Sci Technol, 23(2): 447-456.
• Haymes KM. 1996. Mini-prep method suitable for a plant breeding program. Plant Mol Biol Report, 14(3): 280-284.
• Kadam DC, Lorenz AJ. 2018. Toward redesigning hybrid maize breeding through genomics-assisted breeding. In: Bennetzen J, Flint-Garcia S, Hirsch C, Tuberosa R, eds. The Maize Genome. Cham: Springer, pp: 367-388. https://doi.org/10.1007/978-3-319-97427-9_21.
• Kimura M, Crow JF. 1964. The number of alleles that can be maintained in a finite population. Genetics, 49(4): 725-738. https://doi.org/10.1093/genetics/49.4.725.
• Labroo MR, Studer AJ, Rutkoski JE. 2021. Heterosis and hybrid crop breeding: a multidisciplinary review. Front Genet, 12: 643761.
• Lewontin RC. 1972. Testing the theory of natural selection. Nature, 236(5343): 181-182. https://doi.org/10.1038/236181a0.
• Li G, Quiros CF. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet, 103(2-3): 455-461.
• Li Y, Xue Z, Zhang S, Wen Q. 2018. SRAP analysis on genetic diversity of Brassica juncea. Fujian J Agric Sci, 33(9): 937-942.
• Liu K, Muse SV. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21(9): 2128-2129. https://doi.org/10.1093/bioinformatics/bti282.
• Liu LW, Zhao LP, Gong YQ, Wang MX, Chen LM, Yang JL, Wang LZ. 2008. DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD, ISSR and SRAP markers. Sci Hortic, 116(3): 240-247.
• Malik G, Jabeen A, Mir JI, Shah RA, Shah MA, Dinkar V, Sheikh MA, Kumar R, Sharma OM, Verma MK. 2024. Genetic diversity, population structure and marker-trait associations in Indian kale (Brassica oleracea L. gp. acephala) using cross-species microsatellite markers. Heliyon, 10(8): e29521.
• Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA, 70(12): 3321-3323. https://doi.org/10.1073/pnas.70.12.3321.
• Nieuwhof M. 1969. Cole crops; botany, cultivation and utilization. World Crops Books, London, UK, pp: 353.
• Pipan B, Neji M, Meglič V, Sinkovič L. 2024. Genetic diversity of kale (Brassica oleracea L. var acephala) using agro-morphological and simple sequence repeat (SSR) markers. Genet Resour Crop Evol, 71(3): 1221-1239.
• Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed, 2(3): 225-238.
• Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959. https://doi.org/10.1093/genetics/155.2.945.
• Rohlf FJ. 2000. NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, New York, US.
• Schnable PS, Springer NM. 2013. Progress toward understanding heterosis in crop plants. Annu Rev Plant Biol, 64: 71-88.
• Sneath PHA. 1979. BASIC program for a significance test for clusters in UPGMA dendrograms obtained from squared Euclidean distances. Comput Geosci, 5(1): 127-137. https://doi.org/10.1016/0098-3004(79)90020-7.
• Verhoeven DT, Verhagen H, Goldbohm RA, van den Brandt PA, van Poppel G. 1996. A review of mechanisms underlying anticarcinogenicity by brassica vegetables. Chem Biol Interact, 103(2): 79-129.
• Wu XM, Chen BY, Lu G, Wang HZ, Xu K, Guizhan G, Song Y. 2009. Genetic diversity in oil and vegetable mustard (Brassica juncea) landraces revealed by SRAP markers. Genet Resour Crop Evol, 56: 1011-1022.
• Yeh FC, Yang RC, Boyle TJ, Ye Z, Xiyan JM, Yang R. 2000. POPGENE 32, Microsoft Windows-based freeware for population genetic analysis. Edmonton: Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Canada, pp: 54.
• Yildiz M, Ekbic E, Keles D, Sensoy S, Abak K. 2011. Use of ISSR, SRAP, and RAPD markers to assess genetic diversity in Turkish melons. Sci Hortic, 130(1): 349-353. https://doi.org/10.1016/j.scienta.2011.06.048.
• Zang S, Zhang Y, Guo Y, Hu S. 2019. Genetic diversity pattern of elite lines in Brassica napus L. based on SSR and SRAP markers. J Northwest A & F Univ Nat Sci Ed, 47(5): 7-14.
• Zhang X, Chen H, Channa SA, Zhang Y, Guo Y, Klima M, Yu F, Hu S. 2017. Genetic diversity in Chinese and exotic Brassica rapa L. accessions revealed by SSR and SRAP markers. Braz J Bot, 40: 973-982. https://doi.org/10.1007/s40415-017-0392-1.