Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient

Abstract

Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.

RAD-seq unravels local adaptation along a latitudinal gradient for the wild riceZizania latifolia

“…The RDA analysis showed the environmental factors had a higher contribution com-pared to geographical distance for allele frequency variation, suggesting that IBE better explained the genetic patterns of Z. latifolia although weak IBD was also evident. This result was also supported by the recent SSR study of the species from the similar dis-tribution area (Wagutu et al, 2022). The boundary between the north and south groups is located between the temperate zone and subtropical zone.…”

“…For the 10 Z. latifolia wild populations, the highest level of genetic diversity was found in the populations from the Yangtze River Basin in central China ( H E = 0.146-0.152), which was also evidenced by the recent study based on SSRs (Wagutu et al, 2022; Chen et al, 2017). The Yangtze River Basin is the largest alluvial plain in China.…”

“…The three approaches (Structure, ML tree and PCoA ) consistently showed that all populations were firstly clustered into two clades, the north group and south group, which was also manifested by the recent study based on SSRs (Wagutu et al, 2022). Addi-tionally, the SSRs study further showed that all the individuals from the same population clustered together (Wagutu et al, 2022). This was currently supported by Structure and ML tree, except the individuals from the Zhujiang River Basin.…”

“…Such low num-bers of private alleles have been attributed to genetic similarity within populations, mostly due to isolation and inbreeding (Kalinowski, 2004, Wagutu et al, 2020). Isola-tion and excessive human interference in this region have been cited as the cause of low genetic diversity and differentiation (Wagutu et al, 2022), which could be attributed to the observed low number of private alleles.…”

“…China into approximately eight Eco-geographical zones (Wu et al, 2003), creates unique niches for the species (Wagutu et al, 2022). This climatic isolation coupled with the aforementioned factors such as wetland fragmentation and climate change are the basis for the observed pattern of IBE.…”