Genomic architecture of biomass heterosis in Arabidopsis. Arabidopsis thaliana

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include WUSCHEL, ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative Arabidopsis hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in Arabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions. Overall design: First leaf mRNA profiles of 14-day old A.thaliana Ak-0 and Col-0×Ak-1 were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500.

杂种优势（Heterosis）最常表现为杂交种相较于亲本呈现出显著增强的旺盛生长态势。解析自然种群的基因组变异，是理解植物杂种优势核心分子机制的关键。本研究对200份拟南芥杂交种的生物量杂种优势相关基因组架构进行了系统表征。研究发现，杂交种全基因组杂合度对生物量杂种优势的贡献有限，且未在杂交种中检测到任何表现出明显超显性效应的遗传位点。然而，全基因组关联研究（Genome Wide Association Studies, GWAS）在杂交种中鉴定得到的显著遗传位点的累积效应，与超亲杂种优势（better-parent heterosis, BPH）呈现极强的相关性。
参与生物量超亲杂种优势的候选基因涵盖多种生物学功能，包括细胞过程、代谢途径、发育进程以及应激响应通路。其中重要的杂种优势候选基因包括WUSCHEL、ARGOS，以及一批编码细胞周期调控关键因子的基因。值得注意的是，对代表性拟南芥杂交组合的转录组分析显示，杂种优势候选基因在应激响应通路中显著富集，涵盖生物胁迫响应、非生物胁迫响应与免疫应答等过程。此外，在具备高超亲杂种优势的杂交种中，应激响应基因的表达被抑制至低于亲本的水平；而在无超亲杂种优势的杂交种中，这类基因的表达模式则呈现中亲水平。
本研究揭示了拟南芥生物量杂种优势的基因组调控架构：参与代谢与细胞过程的基因的优势等位基因累积，可提升杂交种的发育与生长水平；而在正常环境条件下，应激响应基因的整体表达抑制，使得杂交种将资源优先分配给生长过程而非环境应激响应。
实验设计：采用Illumina Hiseq 2500平台，对14日龄拟南芥（Arabidopsis thaliana）Ak-0与Col-0×Ak-1的第一片叶进行深度转录组测序，设置两次生物学重复，获取其mRNA表达谱。