Screening of disease-resistant germplasm resources of Pinus massoniana and preliminary SNP analysis based on liquid chip

ZHU Jingyi, LIU Qinghua, ZHOU Zhichun, WANG Yangdong, LUO Dinghui

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (5) : 1-10.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (5) : 1-10. DOI: 10.12302/j.issn.1000-2006.202412002

Screening of disease-resistant germplasm resources of Pinus massoniana and preliminary SNP analysis based on liquid chip

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【Objective】Pinus massoniana (masson pine), a native conifer species endemic to southern China’s mountainous regions, holds significant economic and ecological value. However, the spread of pine wood nematode disease (PWD) has necessitated breeding programs to enhance its resistance, and to provide critical germplasm for PWD-resistant breeding. 【Method】A total of 725 half-sib progenies (from 51 families) derived from PWD-resistant P. massoniana trees were collected across five provinces (cautonomous region). Resistance was assessed via artificial inoculation with 5 000 pine wood nematodes per seedling. Genome-wide association studies (GWAS) were performed by integrating phenotypic data from inoculation assays with targeted sequencing data generated using a 101.6 K liquid-phase probe panel. 【Result】Four highly resistant and ten resistant families were identified as valuable germplasm resources. Statistical analyses revealed that mixed linear model (MLM) obtained five significant SNPs (phenotypic variance explained, PVE 7.69%-11.24%). General linear model (GLM) obtained four significant SNPs (total PVE 5.96%). BLINK model obtained eleven significant SNPs (PVE 12.86%-26.43%). Nine candidate genes were functionally annotated, including P450 family proteins, pectin methylesterase inhibitors (PMEIs), and others. These genes likely regulate post-invasion immune responses by modulating cell wall structure and membrane protein recognition. 【Conclusion】Fourteen P. massoniana resistant families can serve as valuable breeding materials for disease-resistant varieties. Nine candidate disease-resistant genes identified through GWAS will contribute to elucidating the disease resistance mechanisms of P. massoniana and facilitating early selection of disease-resistant varieties.

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masson pine(Pinus massoniana) / pine wilt disease (PWD) / genome-wide association study / resistance genes

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ZHU Jingyi , LIU Qinghua , ZHOU Zhichun , et al . Screening of disease-resistant germplasm resources of Pinus massoniana and preliminary SNP analysis based on liquid chip[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2025, 49(5): 1-10 https://doi.org/10.12302/j.issn.1000-2006.202412002

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
季孔庶, 王章荣, 陈天华, 等. 马尾松扦插繁殖年龄效应及继代扦插复壮效果[J]. 浙江林学院学报, 1999, 16(4):341-345.
JI K S, WANG Z R, CHEN T H, et al. Cyclophysis and effect of rejuvenation with continued cuttage in Pinus massoniana cutting propagation[J]. Journal of Zhejiang Forestry College, 1999, 16(4):341-345. DOI: 10.3969/j.issn.2095-0756.1999.04.003.
Cited in this article [1]
[2]
孙永春. 南京中山陵发现松材线虫[J]. 江苏林业科技, 1982, 9(4):47-27.
SUN Y C. Discovery of Bursaphelenchus xylophilus in Nanjing Sun yat-sen mausoleum[J]. Journal of Jiangsu Forestry Science & Technology, 1982, 9(4):47-27.
Cited in this article [1]
[3]
叶建仁. 松材线虫病在中国的流行现状、防治技术与对策分析[J]. 林业科学, 2019, 55(9):1-10.
YE J R. Epidemic status of pine wilt disease in China and its prevention and control techniques and counter measures[J]. Scientia Silvae Sinicae, 2019, 55(9):1-10.
Cited in this article [1]
[4]
徐将. 松材线虫病疫木就地覆盖熏蒸除害处理技术研究[J]. 现代农业科技, 2017(12):150-151.
XU J. Study on in situ fumigation treatment technology of pine wood nematode infected trees[J]. Modern Agricultural Science and Technology, 2017(12):150-151.
Cited in this article [1]
[5]
颜学武. 花绒寄甲人工饲料及林间应用技术研究[D]. 南京: 南京林业大学, 2014.
YAN X W. A study on the artificial diet and application technology of Dastarcus helophoroides Fairmaire (Coleoptera: Bothrideridae)[D]. Nanjing: Nanjing Forestry University, 2014.
Cited in this article [1]
[6]
陈元生, 黄燕洪, 周满生. 松材线虫病疫木伐桩除害处理技术概述[J]. 林业科技开发, 2014, 28(1): 12-14.
CHEN Y S, HUANG Y H, ZHOU M S. Summary of treatment technology of pine wood nematodes[J]. Forestry science and technology development, 2014, 28(1): 12-14. DOI: 10.13360/j.issn.1000-8101.2014.01.003.
Cited in this article [1]
[7]
ZHAO B G, LI R G. The role of bacteria associated with the pine wood nematode in pathogenicity and toxin-production related to pine wilt[M/OL]// ZHAOB G, KAZUYOSHIF, SUTHERLANDJ R, et al. Pine wilt disease.Tokyo: Springer Japan, 2008.https://doi.org/10.1007/978-4-431-75655-2_24.
Cited in this article [1]
[8]
XIE Y N, LIU B, ZHOU Z C, et al. PmHs1 monitors Bsursaphelenchus xylophilus infection and activates defensive response in resistant Pinus massoniana[J]. Plant,Cell & Environment, 2024, 47(11):4369-4382.DOI: 10.1111/pce.15025.
Cited in this article [1]
[9]
LIU B, XIE Y N, YIN H H, et al. Identification and defensive characterization of PmCYP720B11v2 from Pinus massoniana[J]. International Journal of Molecular Sciences, 2022, 23(12):6640.DOI: 10.3390/ijms23126640.
Cited in this article [1]
[10]
DING L N, LI T, GUO X J, et al. Sclerotinia stem rot resistance in rapeseed:recent progress and future prospects[J]. Journal of Agricultural and Food Chemistry, 2021, 69(10):2965-2978.DOI: 10.1021/acs.jafc.0c07351.
Cited in this article [1]
[11]
WEN Z X, TAN R J, ZHANG S C, et al. Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean[J]. Plant Biotechnology Journal, 2018, 16(11):1825-1835.DOI: 10.1111/pbi.12918.
Cited in this article [2]
[12]
COOPER J S, RICE B R, SHENSTONE E M, et al. Genome-wide analysis and prediction of resistance to goss’s wilt in maize[J]. The Plant Genome, 2019, 12(2):180045.DOI: 10.3835/plantgenome2018.06.0045.
Cited in this article [1]
[13]
NIU S H, LI J, BO W H, et al. The Chinese pine genome and methylome unveil key features of conifer evolution[J]. Cell, 2022, 185(1):204-217.e14.DOI: 10.1016/j.cell.2021.12.006.
Cited in this article [1]
[14]
NEVES L G, DAVIS J M, BARBAZUK W B, et al. Whole-exome targeted sequencing of the uncharacterized pine genome[J]. The Plant Journal, 2013, 75(1):146-156.DOI: 10.1111/tpj.12193.
Cited in this article [1]
[15]
DIAO S, DING X Y, LUAN Q F, et al. Development of 51K liquid-phased probe array for Loblolly and Slash pines and its application to GWAS of Slash pine breeding population[J]. Industrial Crops and Products, 2024, 216:118777.DOI: 10.1016/j.indcrop.2024.118777.
Cited in this article [1]
[16]
LIU B, LIU Q H, ZHOU Z C, et al. Overexpression of geranyl diphosphate synthase (PmGPPS1) boosts monoterpene and diterpene production involved in the response to pine wood nematode invasion[J]. Tree Physiology, 2022, 42(2):411-424.DOI: 10.1093/treephys/tpab103.
Cited in this article [1]
[17]
XIE Y N, LIU B, GAO K, et al. Comprehensive analysis and functional verification of the Pinus massoniana NBS-LRR gene family involved in the resistance to Bursaphelenchus xylophilus[J]. International Journal of Molecular Sciences, 2023, 24(3):1812.DOI: 10.3390/ijms24031812.
Cited in this article [1]
[18]
YANG J, LEE S H, GODDARD M E, et al. GCTA:A tool for genome-wide complex trait analysis[J]. American Journal of Human Genetics, 2011, 88(1):76-82.DOI: 10.1016/j.ajhg.2010.11.011.
Cited in this article [1]
[19]
徐六一, 户田忠雄. 马尾松松材线虫抗性候补木的选拔及评价研究[J]. 安徽农业科学, 2006, 34(17):4303-4304.
XU L Y, HU T. Research on the selection and evaluation of pine wood nematode resistance candidate wood of masson pine[J]. Journal of Anhui Agricultural Sciences, 2006, 34(17):4303-4304.DOI: 10.13989/j.cnki.0517-6611.2006.17.059.
Cited in this article [2]
[20]
CHEN S F, ZHOU Y Q, CHEN Y R, et al. Fastp:an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17):i884-i890.DOI: 10.1093/bioinformatics/bty560.
Cited in this article [1]
[21]
LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14):1754-1760.DOI: 10.1093/bioinformatics/btp324.
Cited in this article [1]
[22]
MCKENNA A, HANNA M, BANKS E, et al. The genome analysis toolkit:a map reduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research, 2010, 20(9):1297-1303.DOI: 10.1101/gr.107524.110.
Cited in this article [1]
[23]
PURCELL S, NEALE B, TODD-BROWN K, et al. PLINK:a tool set for whole-genome association and population-based linkage analyses[J]. The American Journal of Human Genetics, 2007, 81(3):559-575.DOI: 10.1086/519795.
Cited in this article [1]
[24]
EDGARDO M O. Vcf2Phylip V2.0: Convert a vcf matrix into several matrix formats for phylogenetic analysis[J]. 2019. DOI: 10.5281/zenodo.2540861.
Cited in this article [1]
[25]
TAMURA K, STECHER G, KUMAR S. MEGA11:molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 2021, 38(7):3022-3027.DOI: 10.1093/molbev/msab120.
Cited in this article [1]
[26]
LETUNIC I, BORK P. Interactive tree of life (iTOL) v5:an online tool for phylogenetic tree display and annotation[J]. Nucleic Acids Research, 2021, 49(W1):W293-W296.DOI: 10.1093/nar/gkab301.
Cited in this article [1]
[27]
WANG J B, ZHANG Z W. GAPIT version 3:boosting power and accuracy for genomic association and prediction[J]. Genomics,Proteomics & Bioinformatics, 2021, 19(4):629-640.DOI: 10.1016/j.gpb.2021.08.005.
Cited in this article [1]
[28]
NELDER J A, WEDDERBURN R W M. Generalized linear models[J]. Journal of the Royal Statistical Society Series A (General), 1972, 135(3):370.DOI: 10.2307/2344614.
Cited in this article [1]
[29]
LAIRD N M, WARE J H. Random-effects models for longitudinal data[J]. Biometrics, 1982, 38(4):963-974.
Cited in this article [1]
[30]
HUANG M, LIU X L, ZHOU Y, et al. BLINK:a package for the next level of genome-wide association studies with both individuals and markers in the millions[J]. GigaScience, 2019, 8(2):giy154.DOI: 10.1093/gigascience/giy154.
Cited in this article [1]
[31]
QUINLAN A R, HALL I M. BEDTools:a flexible suite of utilities for comparing genomic features[J]. Bioinformatics, 2010, 26(6):841-842.DOI: 10.1093/bioinformatics/btq033.
Cited in this article [1]
[32]
CANTALAPIEDRA C P, HERNÁNDEZ-PLAZA A, LETUNIC I, et al. EggNOG-mapper v2:functional annotation,orthology assignments,and domain prediction at the metagenomic scale[J]. Molecular Biology and Evolution, 2021, 38(12):5825-5829.DOI: 10.1093/molbev/msab293.
Cited in this article [1]
[33]
DONG S S, HE W M, JI J J, et al. LDBlockShow:a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files[J]. Briefings in Bioinformatics, 2021, 22(4):bbaa227.DOI: 10.1093/bib/bbaa227.
Cited in this article [1]
[34]
徐六一. “抗松材线虫病马尾松种源及抗性育种技术研究” 通过验收[J]. 安徽林业科技, 2015, 41(3):20.
XU L Y. The research on the source and resistance breeding technology of masson pine against Pine wood nematode disease has passed the acceptance inspection[J]. Anhui Forestry Science and Technology, 2015, 41(3):20.
Cited in this article [1]
[35]
郝焰平, 徐六一, 姜春武, 等. 安徽省适生马尾松优良种源子代抗松材线虫病评价及生长性状研究[J]. 江西农业学报, 2019, 31(3):41-45.
HAO Y P, XU L Y, JIANG C W, et al. Nematode-resistance evaluation and growth trait study of fine offspring of suitable Pinus massoniana provenances in Anhui Province[J]. Acta Agriculturae Jiangxi, 2019, 31(3):41-45.DOI: 10.19386/j.cnki.jxnyxb.2019.03.07.
Cited in this article [1]
[36]
PANG Y L, LIU C X, LIN M, et al. Mapping QTL for adult-plant resistance to stripe rust in a Chinese wheat Landrace[J]. International Journal of Molecular Sciences, 2022, 23(17):9662.DOI: 10.3390/ijms23179662.
Cited in this article [1]
[37]
ZULAK K G, BOHLMANN J. Terpenoid biosynthesis and specialized vascular cells of conifer defense[J]. Journal of Integrative Plant Biology, 2010, 52(1):86-97. DOI: 10.1111/j.1744-7909.2010.00910.x.
Cited in this article [1]
[38]
GEISLER K, JENSEN N B, YUEN M M S, et al. Modularity of conifer diterpene resin acid biosynthesis:P450 enzymes of different CYP720B clades use alternative substrates and converge on the same products[J]. Plant Physiology, 2016, 171(1):152-164.DOI: 10.1104/pp.16.00180.
Cited in this article [1]
[39]
ZEHRA A, RAYTEKAR N A, MEENA M, et al. Efficiency of microbial bio-agents as elicitors in plant defense mechanism under biotic stress:a review[J]. Current Research in Microbial Sciences, 2021, 2:100054.DOI: 10.1016/j.crmicr.2021.100054.
Cited in this article [1]
[40]
LEE M W, HUFFAKER A, CRIPPEN D, et al. Plant elicitor peptides promote plant defences against nematodes in soybean[J]. Molecular Plant Pathology, 2018, 19(4):858-869.DOI: 10.1111/mpp.12570.
Cited in this article [1]
[41]
宣云, 赵竑绯, 郭肖颖, 等. 植物细胞壁重构酶木葡聚糖内转糖苷酶/水解酶(XTH)的研究进展[J]. 中国农学通报, 2016, 32(18):83-88.
XUAN Y, ZHAO H F, GUO X Y, et al. Plant cell wall remodeling enzyme xyloglucan endotransglucosylase/hydrolase(XTH)[J]. Chinese Agricultural Science Bulletin, 2016, 32(18):83-88.
Cited in this article [1]
[42]
ZHANG X H, LIU Y, AYAZ A, et al. The plant fatty acyl reductases[J]. International Journal of Molecular Sciences, 2022, 23(24):16156.DOI: 10.3390/ijms232416156.
Cited in this article [1]
[43]
LEWANDOWSKA M, KEYL A, FEUSSNER I. Wax biosynthesis in response to danger:its regulation upon abiotic and biotic stress[J]. New Phytologist, 2020, 227(3):698-713.DOI: 10.1111/nph.16571.
Cited in this article [1]
[44]
ARYA G C, SARKAR S, MANASHEROVA E, et al. The plant cuticle:An ancient guardian barrier set against long-standing rivals[J]. Frontiers in Plant Science, 2021, 12:663165.DOI: 10.3389/fpls.2021.663165.
Cited in this article [1]
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