Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 132-143 http://genbreedpublisher.com/index.php/tgmb 132 Feature Review Open Access Conifer Genome Sequencing and Functional Study of Disease Resistance Genes Xiaoqing Tang Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: xiaoqing.tang@hibio.org Tree Genetics and Molecular Breeding, 2024, Vol.14, No.3 doi: 10.5376/tgmb.2024.14.0013 Received: 29 Apr., 2024 Accepted: 31 May, 2024 Published: 08 Jun., 2024 Copyright © 2024 Tang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Tang X.Q., 2024, Conifer genome sequencing and functional study of disease resistance genes, Tree Genetics and Molecular Breeding, 14(3): 132-143 (doi: 10.5376/tgmb.2024.14.0013) Abstract This study reviews recent advances in conifer genome sequencing and the functional study of disease resistance genes. Through the construction of high-density genetic maps, such as those developed for limber pine (Pinus flexilis), numerous key genes involved in disease resistance have been identified, including nucleotide-binding site leucine-rich repeat genes (NBS-LRRs) and receptor-like protein kinase genes (RLKs). These genetic maps provide essential resources for understanding genetic disease resistance and local adaptation to changing climates in conifers. The research also reveals the detailed organization of resistance gene clusters and the genetic mechanisms involved in generating new resistance specificities. The identification of broad-spectrum quantitative disease resistance (BS-QDR) loci in various plants further underscores the potential for similar discoveries in conifers. Success stories, such as the verification of the NBS-LRRgene in pine species for resistance to pine wilt disease, and the PaPR10gene in larch species for resistance to larch needle cast, demonstrate the effectiveness of combining laboratory research with field trials. Future research should focus on the functional validation of identified resistance genes and exploring their roles in conifer disease resistance to accelerate the development of disease-resistant conifer varieties. This study aims to advance the development of conifer genomics and promote its application in practical breeding and conservation efforts. Keywords Conifers; Genome sequencing; Disease resistance genes; High-density genetic maps; Functional genomics 1 Introduction Conifers play a crucial role in global ecosystems and the forestry industry. They are dominant in many forest ecosystems, particularly in the Northern Hemisphere, and provide essential ecological services such as carbon sequestration, habitat for wildlife, and soil stabilization. Economically, conifers are vital for the forestry industry, supplying timber, paper, and other wood products. Their resilience and adaptability to various environmental conditions make them indispensable for both natural and managed forests (Michelmore, 2000; Liu et al., 2019). Despite their importance, understanding conifer genomics and disease resistance poses significant challenges. Conifer genomes are typically large and complex, with high levels of repetitive DNA, making sequencing and assembly difficult. Additionally, the genetic mechanisms underlying disease resistance in conifers are not well understood. This complexity is compounded by the evolutionary pressures exerted by pathogens, which drive the diversification of resistance genes. For instance, the genetic mapping of limber pine has revealed numerous resistance genes, but the functional characterization of these genes remains incomplete (Andolfo et al., 2013; Liu et al., 2019; Kale et al., 2022). Moreover, the identification and functional analysis of resistance genes in other plant species, such as tomato and rice, highlight the intricate regulatory networks and diverse proteins involved in plant immunity, which are likely to be similarly complex in conifers (Wisser et al., 2005; Andolfo et al., 2013). This study is to advance our understanding of conifer genomics and disease resistance through genome sequencing and functional genomics. By leveraging high-throughput sequencing technologies and comprehensive genomic analyses, we aim to identify and characterize resistance genes in conifers. This includes constructing high-density genetic maps, performing genome-wide association studies (GWAS), and elucidating the functional roles of candidate resistance genes. Such efforts will provide valuable genomic resources for breeding and conservation programs, ultimately enhancing the resilience of conifer species to diseases and environmental changes.
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