Gamal El-Dien Omnia, Shalev Tal J, Yuen Macaire M S, Stirling Rod, Daniels Lori D, Breinholt Jesse W, Neves Leandro G, Kirst Matias, Van der Merwe Lise, Yanchuk Alvin D, Ritland Carol, Russell John H, Bohlmann Joerg
Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada.
Pharmacognosy Department, Faculty of Pharmacy Alexandria University Alexandria Egypt.
Evol Appl. 2022 Aug 23;15(8):1291-1312. doi: 10.1111/eva.13463. eCollection 2022 Aug.
Western redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self-compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non-genic regions, we genotyped 44 parent trees and 1520 offspring trees representing 26 polycross (PX) families collected from three progeny test sites using 45,378 SNPs. Trees were phenotyped for eight traits related to growth, heartwood and foliar chemistry associated with wood durability and deer browse resistance. We used the for paternity assignment, maternal pedigree correction, and to estimate genetic parameters. We compared genomics-based (GBLUP) and two pedigree-based (ABLUP: polycross and reconstructed full-sib [FS] pedigrees) models. Models were extended to estimate dominance genetic effects. Pedigree reconstruction revealed significant unequal male contribution and separated the 26 PX families into 438 FS families. Traditional maternal PX pedigree analysis resulted in up to 51% overestimation in genetic gain and 44% in diversity. Genomic analysis resulted in up to 22% improvement in offspring breeding value (BV) theoretical accuracy, 35% increase in expected genetic gain for forward selection, and doubled selection intensity for backward selection. Overall, all traits showed low to moderate heritability (0.09-0.28), moderate genotype by environment interaction (type-B genetic correlation: 0.51-0.80), low to high expected genetic gain (6.01%-55%), and no significant negative genetic correlation reflecting no large trade-offs for multi-trait selection. Only three traits showed a significant dominance effect. GBLUP resulted in smaller but more accurate heritability estimates for five traits, but larger estimates for the wood traits. Comparison between all, genic-coding, genic-non-coding and intergenic SNPs showed little difference in genetic estimates. In summary, we show that GBLUP overcomes the PX limitations, successfully captures expected historical and hidden relatedness as well as linkage disequilibrium (LD), and results in increased breeding efficiency in WRC.
西部红雪松（WRC）是一种在生态和经济方面都很重要的林木树种，其特点是遗传多样性低、自交亲和性高且心材耐久性强。我们利用目标基因和非基因区域的序列捕获基因分型技术，使用45378个单核苷酸多态性（SNP）对来自三个子代测试地点的26个多系杂交（PX）家系的44株亲本树和1520株子代树进行了基因分型。对树木的八个与生长、心材以及与木材耐久性和抗鹿啃食相关的叶化学性质有关的性状进行了表型分析。我们使用该方法进行亲权分配、母系谱系校正，并估计遗传参数。我们比较了基于基因组的（GBLUP）和两种基于谱系的（ABLUP：多系杂交和重建的全同胞[FS]谱系）模型。模型被扩展以估计显性遗传效应。谱系重建揭示了显著的雄性贡献不均，并将26个PX家系分为438个FS家系。传统的母系PX谱系分析导致遗传增益高估高达51%，多样性高估44%。基因组分析使后代育种值（BV）理论准确性提高了高达22%，正向选择的预期遗传增益增加了35%，反向选择的选择强度提高了一倍。总体而言，所有性状的遗传力都较低到中等（0.09 - 0.28），基因型与环境的相互作用中等（B型遗传相关性：0.51 - 0.80），预期遗传增益低到高（6.01% - 55%），并且没有显著的负遗传相关性，这表明多性状选择没有重大权衡。只有三个性状显示出显著的显性效应。GBLUP对五个性状的遗传力估计较小但更准确，但对木材性状的估计较大。对所有、基因编码、基因非编码和基因间SNP的比较表明，遗传估计差异不大。总之，我们表明GBLUP克服了PX的局限性，成功捕获了预期的历史和隐藏的亲缘关系以及连锁不平衡（LD），并提高了西部红雪松的育种效率。
