Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)

Abstract

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.

Genetic Diversity Analysis and Potential Distribution Prediction of Sophora moorcroftiana Endemic to Qinghai–Tibet Plateau, China

“…This may be because there are many mountains with different altitudes in the QTP, which makes the microclimate environment different there, resulting in it becoming the main influencing factor of the plateau plant distribution and gene exchange [27]. However, the result of population genetic diversity of S. moorcroftiana in this study was not quite consistent with a previous study [11], where the He ranged from 0.2956 to 0.3382 compared to 0.437 to 0.539 in this study. This may have been caused by the use of different molecular marker techniques.…”

“…All populations in this study were divided into two groups by genetic structure clustering, while the populations of S. moorcroftiana were clustered into five subgroups in the previous study [11]. Overall, the two groups in this study did not conflict with the five in the previous study.…”

“…Genetic parameters such as Ho, He, F, PPL, Na, Ne, and I are indicators of population genetic diversity [11]. He and H are currently the most widely used parameters, and He is less affected by sample size and can represent population genetic diversity [16].…”

“…It is a low perennial shrub with blue-purple flowers in the leguminous family [10]. This species is mainly distributed in the reaches of the Yarlung Tsangpo River basin with an altitude of 2800-4400 m in the QTP [11]. It has ecological, ornamental, medicinal, and animal feeding values [12,13].…”

“…Therefore, it urgently needs to be conserved. Genetic evolution of plant species in the QTP has been influenced by climate change [11]. Although S. moorcroftiana is a valuable endemic species there, it is at risk of isolation and extinction, and whether its genetic status is affected by climate change remains unclear.…”