PJB-2022-541
EST-SSR marker development based on de novo transcriptomic assembly of Aesculus chinensis Bunge
Yu Ling Li, Xin Mao, Tian Xu Sun, Cui Lan Liu, Yuan Shuai Zhang, Yuan Fu Dong and Xiu Hong Mao
Abstract
Aesculus chinensis Bunge, a deciduous tree in the genus Aesculus of the Hippocastanaceae family, has ornamental, economic, and medicinal values. But the scarcity of comprehensive genetic data hinders the utilization of this species, especially the EST-SSR markers in A. chinensis Bunge have not been reported previously. In this study, the transcriptomes of A. chinensis Bunge were assembled from novo, which enabled the identification of 33,365 unigenes with a mean length of 1348 bp. The sum of 25450 (76.27%) unigenes showed similarities with at least one database including Nr (71.39%), Swiss Prot (57.03%), GO (53.31%), KO (27.13%) and KOG (19.27%). Based on the transcriptome data collected for A. chinensis Bunge, 16,103 SSR loci were detected with a distribution density of one SSR per 2.79 kb. The most dinucleotide and trinucleotide repeats were AG/CT and AAG/CTT. Then 58 primer pairs were randomly selected for polymorphism validation and 31 primer pairs were polymorphic among eight Aesculus samples. There were 167 alleles detected, varying from 2 to 9 with a mean of 5.387 alleles per locus. According to the allelic variation, 7 primers were capable of distinguishing the 8 Aesculus samples from 6 species. These findings will be useful for the conservation, genetic diversity assessment and molecular identification of Aesculus resources.
To Cite this article:
Li, Y.L., X. Mao, T.X. Sun, C.L. Liu, Y.S. Zhang, Y.F. Dong and X.H. Mao. 2024. EST-SSR marker development based on de novo transcriptomic assembly of Aesculus chinensis Bunge. Pak. J. Bot., 56(6): DOI: http://dx.doi.org/10.30848/PJB2024-6(32)
Download
