Development of a 101.6K liquid‐phased probe for GWAS and genomic selection in pine wilt disease‐resistance breeding in Masson pine DOI Creative Commons
Jing-qiu Zhu, Qinghua Liu, Shu Diao

et al.

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: March 1, 2025

Masson pine (Pinus massoniana Lamb.), indigenous to southern China, faces serious threats from wilt disease (PWD). Several natural genotypes have survived PWD outbreaks. Conducting genetic breeding with these resistant holds promise for enhancing resistance in at its source. We conducted a genome-wide association study (GWAS) and genomic selection (GS) on 1013 seedlings 72 half-sib families advance disease-resistance breeding. A set of efficient 101.6K liquid-phased probes was developed single-nucleotide polymorphisms (SNPs) genotyping through target sequencing. inoculation experiments were then performed obtain phenotypic data populations. Our analysis reveals that the targeted sequencing successfully divided experimental population into three subpopulations consistent provenance, verifying reliability probe. total 548 SNPs considerably associated traits using four GWAS algorithms. Among them, 283 located or linked 169 genes, including common plant resistance-related protein such as NBS-LRR AP2/ERF. The DNNGP (deep neural network-based method prediction) model demonstrated superior performance GS, achieving maximum predictive accuracy 0.71. predictions reached 90% top 20% testing ordered by estimated value. This establishes foundational framework advancing research disease-resistant genes P. offers preliminary evidence supporting feasibility utilizing GS early identification individuals.

Language: Английский

Development of a 101.6K liquid‐phased probe for GWAS and genomic selection in pine wilt disease‐resistance breeding in Masson pine DOI Creative Commons
Jing-qiu Zhu, Qinghua Liu, Shu Diao

et al.

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: March 1, 2025

Masson pine (Pinus massoniana Lamb.), indigenous to southern China, faces serious threats from wilt disease (PWD). Several natural genotypes have survived PWD outbreaks. Conducting genetic breeding with these resistant holds promise for enhancing resistance in at its source. We conducted a genome-wide association study (GWAS) and genomic selection (GS) on 1013 seedlings 72 half-sib families advance disease-resistance breeding. A set of efficient 101.6K liquid-phased probes was developed single-nucleotide polymorphisms (SNPs) genotyping through target sequencing. inoculation experiments were then performed obtain phenotypic data populations. Our analysis reveals that the targeted sequencing successfully divided experimental population into three subpopulations consistent provenance, verifying reliability probe. total 548 SNPs considerably associated traits using four GWAS algorithms. Among them, 283 located or linked 169 genes, including common plant resistance-related protein such as NBS-LRR AP2/ERF. The DNNGP (deep neural network-based method prediction) model demonstrated superior performance GS, achieving maximum predictive accuracy 0.71. predictions reached 90% top 20% testing ordered by estimated value. This establishes foundational framework advancing research disease-resistant genes P. offers preliminary evidence supporting feasibility utilizing GS early identification individuals.

Language: Английский

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