基因组选择在林木遗传育种研究中的进展与展望

Recent Advances and Prospect of the Genomic Selection in Forest Genetics and Tree Breeding

基因组选择技术是目前动植物遗传育种的关键技术和研究热点,已在一些动植物的遗传改良工作中取得了重要进展。林木具有世代间隔长的生物学特性,因而育种周期长,早期选择是缩短林木育种周期和加快林木育种进程的有效方法。林木早期选择研究可以粗略分为3个阶段:基于性状表型早晚期相关的早期选择、分子标记辅助选择的早期选择以及基因组选择。林木遗传改良的目标性状主要是生长性状和木材品质性状,其大都是复杂的数量性状,在生长进程中受到更加持久的环境影响。同时生长性状的遗传力是随着生长进程而发生变化的。基因组选择在林木遗传改良中的应用受限于多年生林木自身特点以及研究基础薄弱,包括世代间隔长、体型高大、幼龄期长、基因组和表型组等组学数据匮乏以及相关研究技术平台不完善等因素。为了推动基因组选择技术在林木遗传改良中的应用进程,本文介绍基因组选择技术的原理与方法,总结基因组选择技术在林木遗传育种中的研究进展,探讨基因组选择技术在林木遗传改良中应用的限制性因素。简要介绍基因组选择的线性模型、统计学估计方法(SNP-BLUP、GBLUP和Bayesian估计模型)和分析工具(rrBLUP、synbreed、BGLR、GVCBLUP、GAPIT、sommer和BLUPGA,等)。概括总结基因组选择技术在林木育种中应用的优势,简要概述阔叶树种(杨属、桉属、油棕属和橡胶树属)和针叶树种(松属和云杉属)的基因组选择研究案例,以油棕基因组选择研究作为典型案例分析。林木树种的基因组选择研究案例均表明基因组选择技术有助于提高林木选育效率和加快林木育种进程。深入探讨林木树种的参考基因组、全基因组关联分析、育种群体、连锁不平衡和多年生属性5个方面对林木基因组选择研究的影响。基因组选择在林木遗传育种研究中具有潜在应用前景,但其可行性仍需要大量的模拟数据和真实数据评估。当前林木基因组选择研究所面临的重要问题:1)林木树种的基因组组装质量普遍不高;2)如何开展林木多性状全基因组选择研究;3)针对多年生林木树种自身特点,设计出合理的试验方案,开发具备纵向性状数据处理能力的统计模型和分析软件。

Genomic selection was supposed to be the key technology and hotspot of those studies on animal and plant genetic breeding.Some progress has been made toward the genetic improvement of some animal and plant species.The breeding cycle of tree species is long due to their long generation interval.Early selection is an effective way to shorten the breeding cycle of trees and speed up the breeding process.The studies of early selection of trees can be roughly divided into three stages,including early selection based on the correlation between the early and late trait values,molecular marker-assisted selection and genomic selection.The growth and wood quality traits,the main target traits for tree genetic improvement,are often complex traits controlled by quantitative traits.During the constant process of tree growth and development,these traits are suffered from the on-going influence of the environment.Meanwhile,the heritability of these traits may be gradually changing in the process of tree growth and development.However,the application of genomic selection in tree genetic improvement was limited by the unique characteristic and weak research basis of perennial tree species,such as long generation interval,large body size,long juvenile phase,the lack of multi-omics data(genomic and phenotypic data),and the imperfection of technology platform to facilitate tree researches.To speed the application process of genomic selection in forest genetic improvement,this paper attempts to provide a short overview of the principles and method of whole genomic selection,to summarize recent progress of genome-wide selection in forestry tree genetics and breeding,and to discuss the constraint factors which impact the application of genomic selection in forestry tree genetic improvement.The paper provides a brief introduction of the linear model,statistical estimation methods(SNP-BLUP,GBLUP&Bayesian)and analytical tools(rrBLUP,synbreed,BGLR,GVCBLUP,GAPIT,sommer,BLUPGA and so on)used for genomic selection.It summarizes the advantage of genomic selection applied in forestry tree breeding and the studies of using genomic selection in both broadleaf Populus,Eucalyptus,Elaeis&Hevea)and coniferous(Pinus&Picea)tree species,and dissects these reports of genomic selection in Elaeis guineensis as typical cases.These studies of genomic selection in forestry tree species show that genomic selection contributes to improving the efficiency of forest selection and to accelerating tree breeding.It discusses in detail the possible influence of the tree reference genome,the genome-wide association study,the breeding population,the linkage disequilibrium and the perennial attribute on the genomic selection of trees.Genomic selection has potential application prospects in tree genetics and breeding research.Nevertheless,its feasibility still needs to be further evaluated using vast amounts of simulated and real data.The current research on tree genomic selection is facing multiple challenges:1)a relatively low quality of genome assembly for tree species,2)genomic selection for simultaneously screening multiple target traits,3)the designing of the rational experimental scheme according to the characteristics of the perennial tree species,and the development of the statistical model and analytical tool capable of analyzing the longitudinal character data.