Development of microsatellite markers for partially and putative fully mycoheterotrophic varieties of <i>Pyrola japonica</i> sensu lato (Ericaceae)

Abstract

We developed microsatellite markers to compare the genetic variation and reproductive biology between the partially mycoheterotrophic Pyrola japonica var. japonica and the putative fully mycoheterotrophic P. japonica var. subaphylla. Fifteen primer pairs were developed for P. japonica sensu lato and they were tested on 77 ramets from three populations of the two varieties. Thirteen loci were polymorphic in at least one of the two var. japonica populations, whereas only four loci were polymorphic in the var. subaphylla population. The considerably lower genetic variation of the var. subaphylla population may be attributed to frequent selfing and/or inbreeding. The markers developed in this study will be useful for comparing the genetic diversity of P. japonica s. l. populations and measuring gene flow within and between populations and varieties.

Development of microsatellite markers for the mycoheterotrophic species <i>Burmannia nepalensis</i> (Miers) Hook.f. based on RAD sequencing

“…The average of number of alleles in each population ranged from 2.1 to 2.5; H E varied from 0.335 to 0.396 (Table 2). These values of genetic parameters in B. nepalensis were similar to those reported for other mycoheterotrophic plants, such as Monotropa hypopitys (2.69 for A) (Klooster et al, 2009), Pyrola japonica sensu lato (0.360 for H E ) (Shutoh et al, 2017) and Gastrodia flavilabella (0.444 for H E ) (Tsai et al, 2014). The low genetic variation might be attributed to genetic drift because of the fragmented and small habitats, as mentioned in the study of M. hypopitys (Klooster and Culley, 2010).…”

“…To evaluate the severe impacts of these contributing factors on mycoheterotrophic species, it is important to examine their population genetic diversity, structure and demographic history. However, there exists a major gap in understanding the genetic basis of mycoheterotrophic species: studies on their population genetics have been scarce (Bidartondo, 2005;Klooster et al, 2009), comprising one report for Burmannia wallichii (Zhang and Saunders, 2000) and several for species in the Ericaceae (Klooster and Culley, 2010;Shutoh et al, 2017) and Orchidaceae (Chen et al, 2011;Tsai et al, 2014).…”

Japanese “nameko” mushrooms (<i>Pholiota microspora</i>) produced via sawdust-based cultivation exhibit severe genetic bottleneck associated with a single founder

“…Additionally, while developing the markers, we achieved high rates of success in amplifying the primary candidate markers (21/24 = 0.85) as well as the final set of selected markers (14/24 = 0.58). This result was in contrast to the usual process of our microsatellite marker development, where the ratios of the final selected markers to the primary candidate ones were several to dozens in percentages: 18/45 = 0.40 in Gastrodia takeshimensis (Kishikawa et al, 2019); 13/102 = 0.13 in Phraortes elongatus (Nozaki et al, 2021); 15/293 = 0.05 in Pyrola japonica (Shutoh, Izuno, Isagi, Kurosawa, & Kaneko, 2017); and 26/238 = 0.11 in Cypripedium japonicum (Yamashita, Izuno, Isagi, Kurosawa, & Kaneko, 2016). Our results imply that the Chinese sample used for genome assembly is genetically similar to Japanese samples.…”

Development of microsatellite markers for the completely cleistogamous species <i>Gastrodia takeshimensis</i> (Orchidaceae) that are transferable to its chasmogamous sister <i>G. nipponica</i>

“…Rarity of polymorphic microsatellite loci and high F IS value is also observed in a nearly fully mycoheterotrophic pyroloid, Pyrola subaphylla Maxim. (Shutoh et al, 2017a(Shutoh et al, , 2017b, and it may be one of the typical genetic characteristics of fully mycoheterotrophic plants that inhabit dark understory habitats, which are usually pollinator-limited environments (e.g., Klooster and Culley, 2009;Martos et al, 2015;Suetsugu, 2015).…”