Development and utilization of microsatellite markers to assess genetic variation coupled with modelling range shifts of Dodonaea viscosa (L.) Jacq. in isolated Taita Hills and Mount Kenya forests

• Published in: Molecular biology reports Vol. 49; no. 2; pp. 917 - 929
• Main Authors: Saina, Josphat K., Gichira, Andrew W., Ngarega, Boniface K., Li, Zhi-Zhong, Gituru, Robert W., Hu, Guang-Wan, Liao, Kuo
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-02-2022; Springer Nature B.V
• Subjects: Animal Anatomy; Animal Biochemistry; Biodiversity; Biodiversity hot spots; Biomedical and Life Sciences; Climate change; Conservation of Natural Resources; Dodonaea viscosa; Endangered & extinct species; Flowers & plants; Forests; Genetic diversity; Genetic markers; Genetic resources; Genetic Variation - genetics; Genomes; Habitats; Heterozygosity; High-Throughput Nucleotide Sequencing - methods; Histology; Kenya; Laboratories; Life Sciences; Microsatellite Repeats - genetics; Microsatellites; Molecular biology; Morphology; Mountains; Nucleotide sequence; Original Article; Plant sciences; Polymorphism, Genetic - genetics; Population genetics; Population structure; Sapindaceae - genetics; Kenya; Habitat fragmentation; Population structure; Next-generation sequencing; Simple sequence repeats (SSRs); Dodonaea viscosa
• DOI: 10.1007/s11033-021-06911-y
• EISSN: 1573-4978
• ISSN: 0301-4851

Background
Understanding genetic variation is critical for the protection and maintenance of fragmented and highly disturbed habitats. The Taita Hills of Kenya are the northernmost part of the Eastern Arc Mountains and have been identified as one of the world’s top ten biodiversity hotspots. Over the past century the current forests in the Taita Hills have become highly fragmented. In order to appraise the influence of anthropological disturbance and fragmentation on plant species in these mountains, we studied the genetic variation and population structure of
Dodonaea viscosa
(L.) Jacq. (Sapindaceae), using newly developed microsatellite (SSR) markers, combined with ecological niche modelling analyses (ENMs).
Methods and results
We utilized the Illumina paired-end technology to sequence
D. viscosa's
genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed, and 49,836 SSRs were identified from 42,638 sequences. A total of 18 out of 25 randomly selected primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within populations and only 20% among the eight populations. According to ENM results,
D. viscosa's
suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of (representative concentration pathway) RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments.
Conclusions
In the present study, we successfully developed and tested SSR markers for
D. viscosa.
Study results indicate that fragmentation would constitute a severe threat to plant forest species. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.