Quantitative Trait Loci Analysis Based on High-Density Mapping of Single-Nucleotide Polymorphisms by Genotyping-by-Sequencing Against Pine Wilt Disease in Japanese Black Pine (Pinus thunbergii)

Abstract

Identifying genes/loci for resistance to pine wilt disease (PWD) caused by the pine wood nematode (PWN) is beneficial for improving resistance breeding in Pinus thunbergii, but to date, genetic information using molecular markers has been limited. Here, we constructed a high-density linkage map using genotyping-by-sequencing (GBS) and conducted quantitative trait loci (QTL) analysis for PWD resistance for the self-pollinated progeny of “Namikata 73,” which is the most resistant variety among resistant varieties of P. thunbergii, following inoculation tests with PWN. An S1 mapping population consisting of the 116 progenies derived from self-pollination of the resistant variety, “Namikata 73” (resistance rank 5 to PWN), was inoculated with PWN isolate Ka-4 and evaluated for disease symptoms. To construct a high-density linkage map, we used single-nucleotide polymorphisms (SNPs) identified by GBS based on next-generation sequencing technology and some anchor DNA markers, expressed sequence tag (EST)-derived SNP markers and EST-derived simple sequence repeat (SSR) markers, and genomic SSR markers. The linkage map had 13 linkage groups (LGs) consisting of 2,365 markers including 2,243 GBS-SNP markers over a total map distance of 1968.4 centimorgans (cM). Results from QTL analysis using phenotype data and the linkage map indicated that PWD resistance is controlled by a single locus located on LG-3, as identified in a previous study. This locus showed overdominant genetic action in the present study. With the confirmation of PWD1 in two different mapping populations (present study and a previous study), the locus associated with this region is thought to be a good target for marker-assisted selection in P. thunbergii breeding programs in order to obtain high levels of resistance to PWD caused by PWN.

High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

“…Generally, the density of maps constructed here also compare favourably with recent GBS-or restriction site-associated sequencing (RAD-seq) maps for other forest species. For example, the density of our maps was close to that for Pinus (Hirao et al, 2022) and significantly superior to the Populus maps (Carletti et al, 2016;Xia et al, 2018;Tong et al, 2020).…”

“…Some of the differences in resolution of the genetic maps may be explained by the size of the mapping population ( Yang et al., 2018b ). For example, 1025 F1 progenies were employed in the previous E. urophylla map ( Bartholomé et al., 2015 ), compared with 320 F1 progenies in ours and 130 F1 offspring in Pinus map ( Hirao et al., 2022 ), and 131 to 300 F1 progenies in Populus maps ( Carletti et al., 2016 ; Xia et al., 2018 ; Tong et al., 2020 ). Although preserving large mapping populations is difficult and rarely implemented in forest trees, it may contribute to the accuracy and reliability of genetic linkage mapping and subsequent QTL mapping.…”

“…Moreover, the cost of SNP genotyping continues to fall, with the development of high-throughput technology such as genotyping by sequencing (GBS) ( Elshire et al., 2011 ). Recently, GBS technology has been widely applied to the genotyping of perennial woody plants, such as Eucalyptus ( Brenton et al., 2019 ; Klápště et al., 2021 ), Populus ( Carletti et al., 2016 ; Xia et al., 2018 ), Cinnamomum ( Gong et al., 2021 ) and Pinus ( Hirao et al., 2022 ), accelerating the molecular breeding progress in these species. The publication of the E. grandis reference genome ( Myburg et al., 2014 ) has also significantly aided QTL mapping efforts, with high synteny between E. grandis and other common commercial eucalypts.…”

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

“…It has been discovered that SSRs are ubiquitous in genomes, with repeat units of 1–6 nt. As the most useful DNA marker system for variety identification and germplasm management, SSR molecular markers have several advantages due to their abundance, high polymorphism, multiple alleles, co-dominance, low-cost, and the ease of assay by PCR [ 17 , 18 ], which have been applied extensively in genetic analysis, such as the analysis of population structure and genetic diversity [ 19 , 20 ], QTL mapping [ 21 , 22 , 23 ], marker-assisted selection breeding [ 24 , 25 , 26 ], and DNA fingerprinting [ 27 , 28 ], etc. SSR molecular markers are rarely used in M. incana [ 11 , 14 ], which is largely due to the fact that SSR molecular markers have not been developed in M. incana .…”

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

“…Classical molecular markers due to their low frequency, non-codominant characteristic, and lack of uniform distribution throughout the genome, led to the identification of few QTLs at long genomic distances. NGS-derived SNP markers are free of these weaknesses and can be used to develop high-density maps, e.g., [ 38 , 44 ]. These markers are developed by various NGS-based methods; among them, the GBS method is widely used in QTL mapping (reviewed in [ 34 ]).…”