[1]甘四明.林木分子育种研究的基因组学信息资源述评[J].南京林业大学学报(自然科学版),2020,44(4):001-11.[doi:10.3969/j.issn.1000-2006.202005036]
 GAN Siming.A review on genomics information resources available for molecular breeding studies in forest trees[J].Journal of Nanjing Forestry University(Natural Science Edition),2020,44(4):001-11.[doi:10.3969/j.issn.1000-2006.202005036]
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《南京林业大学学报(自然科学版)》[ISSN:1000-2006/CN:32-1161/S]

卷:
44
期数:
2020年4期
页码:
001-11
栏目:
特邀专论
出版日期:
2020-09-01

文章信息/Info

Title:
A review on genomics information resources available for molecular breeding studies in forest trees
文章编号:
1000-2006(2020)04-0001-11
作者:
甘四明
作者单位:中国林业科学研究院热带林业研究所,热带林业研究国家林业和草原局重点实验室, 广东 广州 510520
Author(s):
GAN Siming
(Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China)
关键词:
林木分子育种 基因组学 连锁作图 关联研究 基因组选择 加速育种
Keywords:
forest tree molecular breeding genomics linkage mapping association studies genomic selection(GS) accelerated breeding
分类号:
S722.3
DOI:
10.3969/j.issn.1000-2006.202005036
文献标志码:
A
摘要:
分子育种是指利用与性状相关的DNA标记进行选育,也称标记辅助选择或标记辅助育种,广义上还包括基因工程育种和基因组学辅助育种。林木分子育种为早期选择和加速育种提供了极具潜力的高效手段。笔者对林木分子育种研究的基因组学信息资源进行了进展综述和前景展望。近30年来,林木分子标记技术从早期的低通量方法发展到目前基于微阵列芯片和新一代测序的高通量技术,如测序分型、转录组测序、重测序、扩增子测序和外显子组测序等,并广泛用于连锁作图、关联分析和基因组选择等林木性状相关的DNA变异检测研究。随着2006年毛果杨基因组序列的发表,已有50余个树种完成了基因组测序。基于连锁作图和关联研究检测了林木10余个属生长、材性和抗逆及非木质产品品质等性状相关的大量基因组位点,主要趋势表现为:① 表型广泛,涵盖经济性状、生理指标和代谢成分等;②标记数量成千上万甚至上百万,覆盖全基因组;③转录组和降解组等多组学的分子变异开始应用;④ 利用大群体以提高位点检测的精度;⑤ 重视环境的影响,大田试验设置多个地点,解析QTL与环境、年份的互作效应;⑥ 结合参考基因组序列和/或转录组差异表达基因进一步挖掘性状相关的候选基因,建立了桉属、松属和云杉属等主要造林树种的基因组选择模型。此外,积累了泛基因组、相关软件和算法、功能基因、基因组编辑技术及网站和数据库等其他信息资源。林木分子育种面临的挑战主要包括:① 如何获得稳定性好的性状相关基因组位点和基因组选择(GS)模型;② 缺乏自动化、无损和高通量的表型测定技术;③对大基因组的针叶树和一些多倍体树种,仍难获得高质量的基因组序列;④ 标记辅助选择增加了常规育种之外的费用,且存在不确定性;⑤多数树种的加速育种仍较困难。后基因组时代的林木分子育种将有效结合到常规育种程序中,显著促进遗传增益的提高。
Abstract:
Molecular breeding refers to selection practices based on DNA markers associated with phenotypic traits, called also as marker assisted selection or marker assisted breeding, in which genetic engineering breeding and geno?mics aided breeding were included in a broad term. It provided a potentially efficient option for early selection and accelerated breeding in forest trees. This review presents the advancement and prospects of genomics information resources for tree molecular breeding studies. In recent three decades, molecular marker techniques have been developed from earlier low-throughput assay to currently high-throughput microarray- and next-generation-sequencing-based platforms, such as genotyping by sequencing, transcriptome sequencing, genome re-sequencing, target amplicon sequencing and exome sequencing, and these high-throughput techniques have been widely used in the three main approaches for identifying trait-related DNA variations in forest trees, including linkage mapping, association genetics and genomic selection studies. More than 50 tree species have been genome sequenced since the first release of Populus trichocarpa whole genome sequence. Linkage mapping and association genetics studies have resulted in many genomic loci related with growth, wood properties and stress responses as well as non-wood product quality traits in more than 10 tree genera, highlighting the trends below: ① a multitude of phenotypic traits investigated, covering economic characteristics, physiological indices and metabolic composition; ② hundreds of thousands of markers across the whole genome scanned; ③ integration of multi-omics data; ④ large population size for high-resolution fine mapping; ⑤ multiple site trials for dissecting the interactions between genotype and environment and between genotype and age; ⑥ mining candidate genes from reference genome sequence and/or differentially expressed transcriptomic genes. Genomic selection models have been formulated for a number of major cultivation tree species in genera Eucalyptus, Pinus and Picea. Other genomic information resour ces such as pan genomes, computational tools and software packages, functional genes, genome editing techniques and online databases have also been available. Challenges that forest tree molecular breeding is facing include:① how to obtain environmentally stable trait-related genomic loci and genomic selection models; ②lacking of autonomous, non-destructive and high-throughput phenotyping methods; ③ difficulty in high-quality genome assembly for genome-large conifers and polyploidy tree species; ④ application uncertainty and balance of additional investment for marker-assisted selection in a breeding program; ⑤ technical barrier in accelerated breeding for most tree species. In the post-genome area, molecular breeding will be integrated effectively into tree breeding programs and can be expected to contribute largely to capturing higher genetic gains as compared to the traditional breeding.

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收稿日期:2020-05-19
更新日期/Last Update: 2020-08-13