Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts

Abstract

The eucalypt species, and, show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross × using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Using Transferable Eucalypt Microsatellite Markers to Identify QTL for Resistance to Ceratocystis Wilt Disease in Eucalyptus pellita F. Muel. (Myrtales, Myrtaceae)

“…The second hypothesis was also confirmed; of the 49 microsatellite markers tested in this study that had been developed in E. grandis, E. urophylla, and E. grandis * E. urophylla, 61% were readily transferred to E. pellita, and of these, 17 could be used to construct a linkage map. This met the expectation that eucalypt species have a microsatellite transferability rate of between 40 and 90% [53], and showed that primer pairs developed to date in these other eucalypt species [7,54] have good transferability to E. pellita, despite the apparent lack of synteny between E. pellita and other eucalypt species. A higher transfer rate may have been achieved if PCR conditions had been optimized to avoid non-specific amplification though the testing of a greater number of markers may be a more efficient strategy.…”

“…In the consensus map of E. grandis with an average distance between markers of 8.4 cM, 10 of the 17 markers that contributed to the two linkage maps of E. pellita in this study have also been found in separate linkage groups, in E. grandis [7,11]. Four of the seventeen markers, EMBRA269, 1364, 1811, and 2014, have been used in the construction of a consensus map [11,54,58]. Three, EMBRA351, EMBRA372 and EUCeSSR071, have not previously been incorporated into linkage maps for other eucalypt species.…”

Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation

“…A subset of 58 primer pairs which were polymorphic in silico in the cross ET86 × EG9 was randomly selected for validating the SSR loci amplification in the 80 full-sib progenies. PCR amplification was performed following the protocol of [29] and the products were separated on 7% polyacrylamide gel electrophoresis. The gel was run at 220 V constant power for 3 h and bands visualised by standard silver staining methods.…”

Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

“…Previous studies on eucalypt using SSR markers include the development of SSR markers (Grattapaglia et al 2015), genetic diversity (Liu et al 2018b), population structure analyses (Costa et al 2017), genetic linkage map (Sumathi et al 2018), phenotypic and genotypic variation (Padovan et al 2017;Zhou et al 2020), and hybrid purity assessment (Subashini et al 2014). However, in Indonesia, there are limited information and studies on the characterization of eucalypts germplasm based on SSR markers such as the genetic diversity of E. urophylla from 7 islands in eastern Indonesia (Payn et al 2007) and genetic variation of E. deglupta, E. urophylla, and E. pellita from arboretum in Yogyakarta as well as seed garden in South Kalimantan (Nurtjahjaningsih et al 2013).…”