A transcriptomic approach to develop a novel set of low-copy nuclear gene primers for the sand whip grass, Psammochloa villosa (Trin.) Bor (poaceae), a dominant species from the inner Mongolia plateau | [Pakistan Journal of Botany • 2023]

Author(s):

1. TING LV: School of Geosciences, Qinghai Normal University,Xining 810008,P. R. China

2. YU-PING LIU: Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Science, Qinghai Normal University,Xining 810008,P. R. China

3. TAO LIU: School of Geosciences, Qinghai Normal University,Xining 810008,P. R. China

4. GUI FU: School of Geosciences, Qinghai Normal University,Xining 810008,P. R. China

5. ZI-LAN MA: Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Science, Qinghai Normal University,Xining 810008,P. R. China

6. CHANG-YUAN ZHENG: Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Science, Qinghai Normal University,Xining 810008,P. R. China

7. XU SU: School of Geosciences, Qinghai Normal University, Xining 810008, P. R. China; 2Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai Tibet Plateau in Qinghai Province, School of Life Science, Qinghai Normal University, Xining 810008, P. R. China; Academy of Plateau Science and Sustainability, Xining 810016, P. R. China; Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai Tibet Plateau, Qinghai Normal University, Xining 810008, P. R. China

Abstract:

The sand whip grass, Psammochloa villosa (Trin.) Bor, is a species found in the Inner Mongolian Plateau and neighboring areas with economic and ecologic importance due to its abundance in sand dunes. Its tolerance to dry environments makes of this grass a species of interest for a potential source of genetic material to improve crops or as a forage plant for local livestock. Here, we designed a collection of primers suitable to amplify genes with the capacity to assess the genetic variability among populations of P. villosa. The primers were designed from a randomly selected subset of 72 low-copy nuclear genes retrieved from 300 orthologs amplified from transcriptomes. We tested the performance of the 10 primers using 15 individuals from five wild populations. The primers were able to amplify ten low-copy genes, whose aligned sequences ranged in length from 716 to 1221 base pairs. We used the resulting data to measure diversity of haplotypes (Hd) and nucleotides (p), which varied from 0.402 to 0.979, and from 0.00064 to 0.006540, respectively. Meanwhile, a phylogenetic analysis showed topological consistency between the topologies of trees constructed using ML and BI methods, placing the genus Achnatherum as sister to Psammochloa. Our work demonstrated the success of these primer pairs amplifying low-copy nuclear genes in P. villosa, and their potential to perform large-scale studies assessing the genetic variation and evolution of this species. These primers may be also useful to conduct molecular studies of closely related taxa such as the numerous and economically important feather grasses in the genus Stipa L.

Page(s): 549-554

DOI: 10.30848/PJB2023-2(2)

Published: Journal: Pakistan Journal of Botany, Volume: 55, Issue: 2, Year: 2023

Keywords:

population genetics , Stipa , Haplotype diversity , phylogenetic relationship , Psammophyte

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