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 ()

Overview

Journal Front Plant Sci

Date 2022 Apr 25

PMID 35463400

Authors

Tomonori Hirao

Koji Matsunaga

Kenta Shirasawa

Affiliations

Soon will be listed here.

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 , 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 , following inoculation tests with PWN. An S 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 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 breeding programs in order to obtain high levels of resistance to PWD caused by PWN.

Citing Articles

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

Zhu X, Weng Q, Bush D, Zhou C, Zhao H, Wang P Front Plant Sci. 2023; 13:1099705.

PMID: 37082511 PMC: 10112524. DOI: 10.3389/fpls.2022.1099705.

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

Tan C, Zhang H, Chen H, Guan M, Zhu Z, Cao X Plants (Basel). 2023; 12(4).

PMID: 36840095 PMC: 9965543. DOI: 10.3390/plants12040748.

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

Younessi-Hamzekhanlu M, Gailing O Int J Mol Sci. 2022; 23(20).

PMID: 36293169 PMC: 9604372. DOI: 10.3390/ijms232012315.

References

Frerot H, Faucon M, Willems G, Gode C, Courseaux A, Darracq A . Genetic architecture of zinc hyperaccumulation in Arabidopsis halleri: the essential role of QTL x environment interactions. New Phytol. 2010; 187(2):355-367. DOI: 10.1111/j.1469-8137.2010.03295.x. View

Birchler J, Yao H, Chudalayandi S . Unraveling the genetic basis of hybrid vigor. Proc Natl Acad Sci U S A. 2006; 103(35):12957-8. PMC: 1559732. DOI: 10.1073/pnas.0605627103. View

Pan J, Wang B, Pei Z, Zhao W, Gao J, Mao J . Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers. Mol Ecol Resour. 2014; 15(4):711-22. DOI: 10.1111/1755-0998.12342. View

Knott S, Marklund L, Haley C, Andersson K, Davies W, Ellegren H . Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics. 1998; 149(2):1069-80. PMC: 1460207. DOI: 10.1093/genetics/149.2.1069. View

Andrews K, Good J, Miller M, Luikart G, Hohenlohe P . Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016; 17(2):81-92. PMC: 4823021. DOI: 10.1038/nrg.2015.28. View

Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter M . Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011; 12(7):499-510. DOI: 10.1038/nrg3012. View

Hirao T, Fukatsu E, Watanabe A . Characterization of resistance to pine wood nematode infection in Pinus thunbergii using suppression subtractive hybridization. BMC Plant Biol. 2012; 12:13. PMC: 3398268. DOI: 10.1186/1471-2229-12-13. View

Wu S, Yang J, Huang Y, Li Y, Yin T, Wullschleger S . An improved approach for mapping quantitative trait Loci in a pseudo-testcross: revisiting a poplar mapping study. Bioinform Biol Insights. 2010; 4:1-8. PMC: 2832300. DOI: 10.4137/bbi.s4153. View

Liu H, Bayer M, Druka A, Russell J, Hackett C, Poland J . An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics. 2014; 15:104. PMC: 3922333. DOI: 10.1186/1471-2164-15-104. View

10.

JONES D . Dominance of Linked Factors as a Means of Accounting for Heterosis. Proc Natl Acad Sci U S A. 1917; 3(4):310-2. PMC: 1091241. DOI: 10.1073/pnas.3.4.310. View

11.

Neves L, Davis J, Barbazuk W, Kirst M . A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. G3 (Bethesda). 2013; 4(1):29-37. PMC: 3887537. DOI: 10.1534/g3.113.008714. View

12.

Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E . A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011; 6(5):e19379. PMC: 3087801. DOI: 10.1371/journal.pone.0019379. View

13.

Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E . TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19):2633-5. DOI: 10.1093/bioinformatics/btm308. View

14.

Bartholome J, Mandrou E, Mabiala A, Jenkins J, Nabihoudine I, Klopp C . High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol. 2014; 206(4):1283-96. DOI: 10.1111/nph.13150. View

15.

Hirao T, Matsunaga K, Hirakawa H, Shirasawa K, Isoda K, Mishima K . Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii). BMC Plant Biol. 2019; 19(1):424. PMC: 6792208. DOI: 10.1186/s12870-019-2045-y. View

16.

He J, Zhao X, Laroche A, Lu Z, Liu H, Li Z . Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci. 2014; 5:484. PMC: 4179701. DOI: 10.3389/fpls.2014.00484. View

17.

Hayashi E, Kondo T, Terada K, Kuramoto N, Kawasaki S . Identification of AFLP markers linked to a resistance gene against pine needle gall midge in Japanese black pine. Theor Appl Genet. 2004; 108(6):1177-81. DOI: 10.1007/s00122-003-1537-0. View

18.

Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J . A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. Plant J. 2017; 90(1):189-203. DOI: 10.1111/tpj.13478. View

19.

Nicotra A, Chong C, Bragg J, Ong C, Aitken N, Chuah A . Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium. Mol Ecol. 2016; 25(9):2000-14. DOI: 10.1111/mec.13584. View

20.

Lu Q, Cui Y, Wu R . A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genet. 2004; 5:20. PMC: 509239. DOI: 10.1186/1471-2156-5-20. View